There was one time I got several levels up at once (one right after another) and somehow the level up menu got stuck on screen while I was playing. I could move the character and the game was running like normal, but with the level up menu on top.
Nothing was highlighted (no yellow border and pressing directions didn't select any of the options). Pressing Y got rid of the level up menu. Pressing A was doing anything. I hadn't tried pressing any other buttons before pressing Y.
I realized at the next level up that pressing Y did use up a skip.
(I hope I'm not being annoying. I'm assuming this sort of stuff is helpful to know).
Edit: It happened again. This time I had all items at max, so I was getting the gold/health option every level up. After at least five times of quickly pressing A to get gold, the level up tone sounded again but the yellow selection outline went away.
The level up menu was stuck on screen again even though the game was no longer paused. Pausing and unpausing doesn't et rid of it. Getting another level up makes the yellow selection border show up again. and does let you select and choose the level up option. But the level up menu remains on screen even though the gameplay resumes.
This time I pressed X and it rerolled, which brought back the yellow selection border and let me complete the level up so it would go away.
I think if that were ever to happen when you have no reroll, skip, or banish remaining that there would be no way to get rid of the level up menu at all.
I don't know what's causing it (honestly it's so weird), but putting in a check to see if the level up menu is ever up but there is nothing selected might find/fix it.
Edit2: It happened again. I got seven level ups in a roll, and it broke (stuck on screen). I made sure to press A slowly this time, so it is NOT the speed at which A is being pressed that causes it.
That games moves forwards what looks like several frames of gameplay in between every level up. Maybe that has something to do with why getting at least six or seven level ups in a row can break the level up menu?
I also realized banish can't be used to get rid of it when it's stuck. So only reroll and skip can fix it.