I have no idea how this could be, so closing as unreproducible.

Funny, I found out how to reproduce in 45 seconds ;) There are several different variations, I even managed to create a level=;2 + addr:floor=1;1 situation. The key step seems to be that you initially have to provide addr:floor by typing in the manual editor, return to map by pressing Save, and then reenter the editor and choose another option for level or level + addr:floor from the options that are suggested next to the steps icon (I honestly don't fully understand when these options appear and when not 😅). I'm sure you're figure it out with this hint, but anyway here's one step-by-step description:

1. Find an amenity with no addr:floor or level tag that already has suggestions for these tags in the main amenity editor screen.
2. Add value 3 for addr:floor by typing in the manual editor screen addr:floor and level. Observe value 3/ being highlighted next to the steps icon in the amenity editor screen.
3. Press Save and exit amenity editor.
4. Enter amenity editor again. Observe value 3/ still being highlighted next to the steps icon in the amenity editor screen.
5. Choose a suggested /1 option that adds a value for level. Observe /1 being highlighted, but but 3/ being not anymore.
6. Go to diff/history screen and observe local changes: addr:floor=;3 + level=1.
7. Choose a suggested /-1 option that adds a value for level. Observe both /-1 and /1 being highlighted (!).
8. Go to diff/history screen and observe local changes: level=-1;1, addr:floor missing.

This is mind-bending. I'll reopen this, but will come back some other day, with a clear head :)

I even managed to create a level=;2

For clarity: