MacOS – Why is the Partition a folder

I've set up a iMac12,1 with Yosemite (fresh) on a second partition.
Then I've formatted my first partition (after i migrated my data from my old installation to my Yosemite installation on the 2nd partition)

After formatting, I am presented by a Folder icon in Disk Utility:

But to actually access the folder i had to chown it to my user.
What is happening here? The mac also randomly choses to fail at the boot screen, but after some fsck -fy in SU mode it boots again like nothing happened.

UPDATE:
Tried formatting the partition again, now i get an error saying that the media cannot be deactivated. I guess OSX just recognizes that this is indeed a folder and unmounting a folder leads to this error.
Another thing what striked me: there are apparently 132.629 Folders in this partition (disk utility says that)

diskutil list:

/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *1.0 TB     disk0
   1:                        EFI EFI                     209.7 MB   disk0s1
   2:                  Apple_HFS HDD                     499.7 GB   disk0s2
   3:                  Apple_HFS Yosemite                499.0 GB   disk0s3
   4:                 Apple_Boot Recovery HD             650.0 MB   disk0s4
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *1.1 TB     disk1
   1:                        EFI EFI                     209.7 MB   disk1s1
   2:                  Apple_HFS Disk Image              1.1 TB     disk1s2

diskutil cs list:

No CoreStorage logical volume groups found

/etc/auto_master:

cat /etc/auto_master
#
# Automounter master map
#
+auto_master        # Use directory service
/net            -hosts      -nobrowse,hidefromfinder,nosuid
/home           auto_home   -nobrowse,hidefromfinder
/Network/Servers    -fstab
/-          -static

diskutil info /Volumes/HDD

diskutil info /Volumes/HDD
Could not find disk: /Volumes/HDD

diskutil info disk0s2

diskutil info disk0s2
   Device Identifier:        disk0s2
   Device Node:              /dev/disk0s2
   Part of Whole:            disk0
   Device / Media Name:      Customer

   Volume Name:              HDD

   Mounted:                  Yes
   Mount Point:              /Volumes/HDD

   File System Personality:  Journaled HFS+
   Type (Bundle):            hfs
   Name (User Visible):      Mac OS Extended (Journaled)
   Journal:                  Journal size 90112 KB at offset 0x1980f000
   Owners:                   Enabled

   Partition Type:           Apple_HFS
   OS Can Be Installed:      Yes
   Media Type:               Generic
   Protocol:                 SATA
   SMART Status:             Verified
   Volume UUID:              3B40521B-D7F0-3924-9F4E-D9A9FC2FEC16
   Disk / Partition UUID:    00004DD6-4AB2-0000-A05F-0000E4410000

   Total Size:               499.7 GB (499672563712 Bytes) (exactly 975922976 512-Byte-Units)
   Volume Free Space:        863.4 GB (863430361088 Bytes) (exactly 1686387424 512-Byte-Units)
   Device Block Size:        512 Bytes
   Allocation Block Size:    4096 Bytes

   Read-Only Media:          No
   Read-Only Volume:         No
   Ejectable:                No

   Whole:                    No
   Internal:                 Yes
   Solid State:              No

UPDATE:
I had a Applescript mounting a sparsebundle Image from a Samba Server for Time Machine Backups (see @klanomath's answer)
This script uses perl to execute a system command – hdiutil attach
I don't know why, but the existing Mountpoints somehow get messed up when using this script.
After updating it with @klanomath's suggestion, Time Machine still runs fine and the mounts in /Volumes seem correct, but the script seems to mirror all of my Volumes in /Volumes/HDDBackup. Look at them:

ls -la /Volumes/HDDBackup/

total 2680
drwxrwxrwt+ 15 root        admin                           578 Nov  5 17:02 .
drwxrwxrwt@  6 root        admin                           204 Nov  6 08:31 ..
-rw-r--r--@  1 mgottstein  Domänen-Benutzer    10244 Nov  4 08:25 .DS_Store
drwx------   5 root        Domänen-Benutzer      170 Oct 30 13:05 .Spotlight-V100
d-wx-wx-wt   3 mgottstein  Domänen-Benutzer      102 Nov  3 16:17 .Trashes
-rw-r--r--   1 root        wheel                       1228840 Sep 20 04:41 .VolumeIcon.icns
-rw-r--r--   1 root        Domänen-Benutzer      629 Oct 30 18:20 .disk_label
-rw-r--r--   1 root        Domänen-Benutzer     2525 Oct 30 18:20 .disk_label_2x
drwx------  29 mgottstein  Domänen-Benutzer      986 Oct 30 16:03 .fseventsd
drwxr-xr-x+  6 root        Domänen-Benutzer      204 Nov  5 09:49 Backups.backupdb
drwxrwxrwx   3 mgottstein  Domänen-Benutzer      102 Nov  3 16:18 HDD
d--x--x--x+  4 root        admin                           136 Nov  5 17:05 HDD1
-rwxr-xr-x@  1 root        wheel                        115716 Sep 20 09:26 tmbootpicker.efi

The System now runs without a hiccup for now, only Disk Utility seems confused – it takes a minute to load the Volumes. I can live with that 🙂 thanks @klanomath!

Thanks!