MacOS – Mojave has apps in a zombie state, neither launched nor quit

I'm experiencing an unusual problem that is affecting many of the apps I use on a regular basis, including (but not limited to): Adobe Illustrator CC 2019, Sublime Text 3, FileZilla, and even Apple's native TextEdit! The sequence of events goes something like this:

1. An app freezes and I must Force Quit out of it.
2. I try to re-launch the app, but the icon just bounces in the Dock endlessly (until I Force Quit again)
3. I try to Shut Down the Mac, but macOS insists it can't shut down because said app is still running (although it shouldn't be, since I did a Force Quit). Also, no dot is shown below the app's Dock icon, leading one to believe it is not open, but it's still running.
4. I must physically hold the power button to shut down.

^ ^{As you can see, the application is "Not Responding". But there is no dot below to indicate it is even open to begin with.}

I have tried to Force Quit the app(s) in question via Terminal as well, after identifying their Process IDs. Unfortunately, this has not worked either.

Further Details

macOS is the most current version to date: Mojave 10.14.2

This iMac shipped with High Sierra and I immediately updated it to Mojave before beginning to use it. This problem came to my attention after less than 1 month of use. I updated Mojave to 10.14.2 hoping it would fix the problem, however the problem persists. The Mac is just over 2 months old.

Freezing/hanging often often occurs upon saving a file. The file gets saved, but immediately after that the app (whichever app it is) becomes unusable. The problem seems to be closely tied to the file system.

^ ^{It is usually right after saving a file that problems begin.}

This is a work machine, and one other employee at the company is experiencing the same issue with Mojave (on an older Mac). We both connect to the company LAN, and do Time Machine backups over the LAN.

According to Disk Utility, nothing appears to be wrong with Macintosh HD:

Running First Aid on “Macintosh HD” (disk2s1)

NOTE: First Aid will temporarily lock the startup volume.

Verifying file system.
Volume could not be unmounted.
Using live mode.
Performing fsck_apfs -n -l -x /dev/rdisk2s1
Checking the container superblock.
Checking the fusion superblock.
Checking the EFI jumpstart record.
Checking the space manager.
Checking the space manager free queue trees.
Checking the object map.
Checking the Fusion data structures.
Checking volume.
Checking the APFS volume superblock.
The volume Macintosh HD was formatted by hfs_convert (945.200.129) and last modified by apfs_kext (945.230.6).
Checking the object map.
Checking the snapshot metadata tree.
Checking the snapshot metadata.
Checking snapshot 1 of 2.
Checking snapshot 2 of 2.
Checking the extent ref tree.
Checking the fsroot tree.
Verifying allocated space.
Performing deferred repairs.
The volume /dev/rdisk2s1 appears to be OK.
File system check exit code is 0.

Operation successful.

Crash report comparison

There's a lot of data to sort through, in crashes for multiple applications, so while it's hard to know what exactly to look for, the following lines look like they might provide a clue.

I used Compare Side-By-Side in Sublime Text. Text highlighted in darker pink and darker green is dissimilar. Text highlighted in lighter pink and lighter green is similar. White text is identical.

Here's more information from the log on the left side, which happens to be TextEdit, the third crash I experienced on 2019-01-29.

I will include the portion for processes diskarbitrationd [67] and diskimages-helper [2452] because there is a lot of correlation there with the FileZilla crash one day prior.

Process:         diskarbitrationd [67]
UUID:            6A57BB14-2FB6-3420-ABDA-429D1991CFE3
Path:            /usr/libexec/diskarbitrationd
Architecture:    x86_64
Parent:          launchd [1]
UID:             0
Sudden Term:     Tracked
Footprint:       2016 KB
Start time:      2019-01-29 09:26:56 +0900
End time:        2019-01-29 09:26:58 +0900
Num samples:     17 (1-17)
Note:            1 idle work queue thread omitted

  Thread 0x252              DispatchQueue 1           17 samples (1-17)         priority 31 (base 31)
  <thread QoS default (requested default), process sudden termination dirty, IO tier 0>
  17  start + 1 (libdyld.dylib + 93913) [0x7fff5cd86ed9] 1-17
    17  ??? (diskarbitrationd + 29299) [0x10731d273] 1-17
      17  ??? (diskarbitrationd + 31571) [0x10731db53] 1-17
        17  CFRunLoopRun + 40 (CoreFoundation + 240468) [0x7fff2fb48b54] 1-17
          17  CFRunLoopRunSpecific + 463 (CoreFoundation + 240968) [0x7fff2fb48d48] 1-17
            17  __CFRunLoopRun + 1654 (CoreFoundation + 243217) [0x7fff2fb49611] 1-17
              17  __CFRunLoopServiceMachPort + 337 (CoreFoundation + 245954) [0x7fff2fb4a0c2] 1-17
                17  mach_msg_trap + 10 (libsystem_kernel.dylib + 4474) [0x7fff5cec017a] 1-17
                 *17  ipc_mqueue_receive_continue + 0 (kernel + 1651312) [0xffffff8000393270] 1-17

  Binary Images:
           0x107316000 -        0x10732efff  diskarbitrationd (297.200.5)        <6A57BB14-2FB6-3420-ABDA-429D1991CFE3>  /usr/libexec/diskarbitrationd
        0x7fff2fb0e000 -     0x7fff2ff5bfff  com.apple.CoreFoundation 6.9 (1561) <AC90EE38-93D9-35EF-8359-9FE3A42500D4>  /System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation
        0x7fff5cd70000 -     0x7fff5cd9ffff  libdyld.dylib (640.2)               <376E3F3A-6942-3B0E-AD5E-4B97E8255CF5>  /usr/lib/system/libdyld.dylib
        0x7fff5cebf000 -     0x7fff5cee7fff  libsystem_kernel.dylib (4903.231.4) <ABDAABCA-C22A-3960-AA4E-E91A9FF34929>  /usr/lib/system/libsystem_kernel.dylib
   *0xffffff8000200000 - 0xffffff8000bfffff  kernel (4903.231.4)                 <56B30885-F9BA-30E8-AD1C-5D59EC243BA9>  /System/Library/Kernels/kernel


Process:         diskimages-helper [2452]
UUID:            215C14BD-2ABA-36D8-AE6C-6279F4082D96
Path:            /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/Resources/diskimages-helper
Architecture:    x86_64
Parent:          launchd [1]
Responsible:     backupd [2395]
UID:             0
Footprint:       4080 KB
Start time:      2019-01-29 09:26:56 +0900
End time:        2019-01-29 09:26:58 +0900
Num samples:     17 (1-17)
Note:            1 idle work queue thread omitted

  Thread 0x4f9a             17 samples (1-17)         priority 20 (base 20)
  <thread QoS utility (requested utility), timers tier 3 (coalesced), IO tier 3>
  17  <truncated backtrace> 1-17
    17  mach_msg_trap + 10 (libsystem_kernel.dylib + 4474) [0x7fff5cec017a] 1-17
     *17  ipc_mqueue_receive_continue + 0 (kernel + 1651312) [0xffffff8000393270] 1-17

  Thread 0x4f9e             17 samples (1-17)         priority 20 (base 20)
  <thread QoS utility (requested default), timers tier 3 (coalesced), IO tier 3 and passive>
  17  thread_start + 13 (libsystem_pthread.dylib + 9237) [0x7fff5cf79415] 1-17
    17  _pthread_start + 70 (libsystem_pthread.dylib + 25199) [0x7fff5cf7d26f] 1-17
      17  _pthread_body + 126 (libsystem_pthread.dylib + 13061) [0x7fff5cf7a305] 1-17
        17  __NSThread__start__ + 1218 (Foundation + 73988) [0x7fff31ea5104] 1-17
          17  ??? (diskimages-helper + 52345) [0x106fb1c79] 1-17
            17  ??? (diskimages-helper + 55130) [0x106fb275a] 1-17
              17  DI_kextDriveGetRequest + 43 (DiskImages + 114665) [0x7fff4537cfe9] 1-17
                17  IOConnectCallStructMethod + 38 (IOKit + 34474) [0x7fff325906aa] 1-17
                  17  IOConnectCallMethod + 244 (IOKit + 32413) [0x7fff3258fe9d] 1-17
                    17  io_connect_method + 374 (IOKit + 32827) [0x7fff3259003b] 1-17
                      17  mach_msg_trap + 10 (libsystem_kernel.dylib + 4474) [0x7fff5cec017a] 1-17
                       *17  hndl_mach_scall64 + 22 (kernel + 1426566) [0xffffff800035c486] 1-17
                         *17  mach_call_munger64 + 555 (kernel + 2889483) [0xffffff80004c170b] 1-17
                           *17  mach_msg_overwrite_trap + 910 (kernel + 1717662) [0xffffff80003a359e] 1-17
                             *17  ipc_kmsg_send + 549 (kernel + 1633253) [0xffffff800038ebe5] 1-17
                               *17  ipc_kobject_server + 301 (kernel + 1786557) [0xffffff80003b42bd] 1-17
                                 *17  ??? (kernel + 2706356) [0xffffff8000494bb4] 1-17
                                   *17  is_io_connect_method + 527 (kernel + 8972575) [0xffffff8000a8e91f] 1-17
                                     *17  IOUserClient::externalMethod(unsigned int, IOExternalMethodArguments*, IOExternalMethodDispatch*, OSObject*, void*) + 832 (kernel + 8934912) [0xffffff8000a85600] 1-17
                                       *17  shim_io_connect_method_structureI_structureO + 460 (kernel + 8942556) [0xffffff8000a873dc] 1-17
                                         *17  IOHDIXHDDriveOutKernelUserClient::getRequest64(HDIRequestOOL64 const*, HDIRequestOOL64*) + 257 (IOHDIXController + 11293) [0xffffff7f86529c1d] 1-17
                                           *17  IOHDIXHDDriveOutKernel::getRequest(HDIRequestOOL64*, IOMemoryDescriptor*) + 31 (IOHDIXController + 7179) [0xffffff7f86528c0b] 1-17
                                             *17  ??? (kernel + 1926025) [0xffffff80003d6389] 1-17
                                               *17  thread_block_reason + 175 (kernel + 1876623) [0xffffff80003ca28f] 1-17
                                                 *17  ??? (kernel + 1881552) [0xffffff80003cb5d0] 1-17
                                                   *17  machine_switch_context + 195 (kernel + 2970867) [0xffffff80004d54f3] 1-17

  Binary Images:
           0x106fa5000 -        0x106ff2fff  diskimages-helper (480.230.2)                       <215C14BD-2ABA-36D8-AE6C-6279F4082D96>  /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/Resources/diskimages-helper
        0x7fff31e93000 -     0x7fff32261fff  com.apple.Foundation 6.9 (1561)                     <27FD022F-F0E3-3053-BADA-DF9BF856CA85>  /System/Library/Frameworks/Foundation.framework/Versions/C/Foundation
        0x7fff32588000 -     0x7fff3261afff  com.apple.framework.IOKit 2.0.2 (1483.230.1)        <AAAF13D1-80E5-3079-98C1-FA3C3FC47B40>  /System/Library/Frameworks/IOKit.framework/Versions/A/IOKit
        0x7fff45361000 -     0x7fff45433fff  com.apple.DiskImagesFramework 480.230.2 (480.230.2) <829D174B-D19D-3302-8C66-0FAD8DF43A6F>  /System/Library/PrivateFrameworks/DiskImages.framework/Versions/A/DiskImages
        0x7fff5cebf000 -     0x7fff5cee7fff  libsystem_kernel.dylib (4903.231.4)                 <ABDAABCA-C22A-3960-AA4E-E91A9FF34929>  /usr/lib/system/libsystem_kernel.dylib
        0x7fff5cf77000 -     0x7fff5cf81fff  libsystem_pthread.dylib (330.230.1)                 <BA382BFC-6A17-3940-B417-D090EF2AF4F4>  /usr/lib/system/libsystem_pthread.dylib
   *0xffffff7f86527000 - 0xffffff7f86532fff  com.apple.driver.DiskImages 493.0.0 (493.0.0)       <81642D4E-F204-3227-8B31-BFC8CD1DDC32>  /System/Library/Extensions/IOHDIXController.kext/Contents/MacOS/IOHDIXController
   *0xffffff8000200000 - 0xffffff8000bfffff  kernel (4903.231.4)                                 <56B30885-F9BA-30E8-AD1C-5D59EC243BA9>  /System/Library/Kernels/kernel

There are many other processes ending up like this: <thread QoS default (requested default), process sudden termination dirty, IO tier 0>

As follows are the processes that had dirty termination (while I don't understand exactly what that means, it doesn't sound good). Listed chronologically:

ACCFinderSync [535]
authd [136]
com.apple.AmbientDisplayAgent [360]
com.apple.appkit.xpc.openAndSavePanelService [53178]
com.apple.ctkpcscd [171]
com.apple.dock.extra [541]
coreaudiod [161]
corespotlightd [744]
CVMServer [317]
diskarbitrationd [67]
distnoted [103]
distnoted [359]
distnoted [397]
distnoted [840]
filecoordinationd [461]
fileproviderd [947]
Finder [525]
imklaunchagent [454]
IMRemoteURLConnectionAgent [433]
IMRemoteURLConnectionAgent [444]
IMRemoteURLConnectionAgent [475]
mds_stores [337]
nsurlsessiond [187]
nsurlsessiond [411]
nsurlstoraged [425]
opendirectoryd [75]
PAH_Extension [455]
pboard [442]
pkd [451]
rapportd [396]
securityd [81]
sharingd [431]
spindump [346]
symptomsd [191]
syslogd [39]
thermald [313]
useractivityd [435]
ViewBridgeAuxiliary [447]
WiFiProxy [544]

Update

I have some good news, which is that since turning off automatic Time Machine backups I have not had this problem! But I still would like to know the cause of it, and if there's a way to still run scheduled Time Machine backups over the network without experiencing severe system problems. I can provide more details upon request.