I think I figured it out with the disk usage app. According to disk usage, there is a storage calculation for apps. Under system settings this is calculated by the size of the apk files which are like .exe programs on windows. Each app has a certain amount of files that it needs to run. In windows, you have an .exe file and then you have a ton of other files which actually run the .exe like .dll and such. The misc file calculation seems to be those extra files to run the apk. The best example I can think of is like when you install a game like Brave Frontier. You install the apk file off of google play, however, when you first run Brave Frontier, it will download like 100 extra files before you can play the game. In storage, the apk is filed under app storage, but the 100 extra files are calculated as misc file storage. If you move apps to an external sd card, it will move the apk and run it off of the sd card. The extra/misc files stay on the internal memory of the phone. I have a Samsung Note 5 and it seems that when I install a new app, the system memory allotted to apps goes up as well as the misc file. When I uninstall the the same app, both app file memory and misc file memory go down by the same amount it went up when I installed it. I hope this makes sense.
Chris