<Watching this thread>
I have see other files end up in the wrong place (usually Misc).
I suspect the Manifest was wrong, thus the mess I see.
I
tried Dragging from Misc to 'CSS' or 'Fonts' (those the usual culprits true home). No joy.
Right click offers no (Move to, Reclassify) solution.
For some files, I exported (to desktop), Then Added them back, where they landed in the proper place
SAVE Before trying
For your 'mimetype' file, I suspect the Remove option shown will force a new one to be generated on the next save