I think you've got a double assignment
If you assign a file to a display group, then that doesn't then show up if you look at an individual display. It's held on the group itself and merged in as the Players call Required Files. In exactly the same way as if you schedule a layout to a display group it doesn't show up on the individual display (as it's not held there).
What I think you're seeing is that when you set Version instructions on a Display, it will automatically assign the correct apk file to the Display to ensure that the file is there when the upgrade tries to run.
You're then removing the assignment from the Display Group thinking it's the same one as you can see in the Display record (but it isn't).