MacOS – Files such as com.apple.finder or com.apple.dock

You have discovered iTrash which searches for related files at the time when you want to delete an application.

There are also uninstall apps which track all files used by an application. So they have a daemon (or helper app) which runs in the background all the time. Synium's Clean App works in this way - that is what I use.

Even better read the answers to How do I uninstall a program completely on a Mac? That covers it pretty well.

I realised that the only volume I was having issues with was a NTFS-formatted volume, for which I use Paragons software to write to the volume. I searched for a solution to my problem and found someone having the same problem: http://forums.macrumors.com/showthread.php?t=1280829

It turns out Paragon writes the files with read, write flags, AND also the execute flag, which causes the files to not be recognised by the Finder. To solve this, you simply have to put the flags to read and write using chmod 644.

Thanks for all the help!