I'm using the Windows version but it's through WINE on Pop!_OS 20.10, so this might be on me if it's not reproducible on native Windows.
I reached the final heart on Extra, but the boss ran off-screen and bullets stopped appearing. 
As far as regular story mode goes, I was in the first stage on Overdrive. I died, continued, and then noticed I wasn't doing any damage so I got killed again to see if going back to the menu fixed it. I was then stuck at the tutorial pattern without being able to deal damage until I Alt-F4ed.
Viewing post in When Witches Fly - 太陽が西から昇る jam comments
Alright, thanks for letting me know. The first is an bug that I remembering happening on both the first stage boss and the extra stage boss but apparently only implemented the fix for with the latter. If you do want to play the extra boss some more, you’ll have to hang out on the lower half of the screen and wait for them to start coming towards you. Once you deal some damage to them after that they should travel to the right but not off screen. (Very odd and specific advice I know)
The other I’ll have to look into because I’ not entirely sure why that happens. Glad you found a way around it I’ll have to put some kind of warning about that in a readme file.