I think it was the second level with spikes, I had accidentally set the gravity to negative so the box I had selected floated up. Then I scaled it up (if I remember correctly it might have been partially inside the spikes). Then I attempted to scale it down, after a few scale reductions everything froze.
Its been a few hours so I don't quite remember everything, but hopefully that helps!
I still can't seem to find that bug that you're talking about 😅 Were you playing without fullscreen enabled, web version? That might be the problem if your cursor is near the submission button (see image), the game window might be unfocused (this is itch's fault)