When either stopping the brainfuck code using "stop" or it crashes because of a runtime error, pretty much every time all breakpoints become ghosts.
What I mean by ghosts is that the characters are still red, but you can't remove the breakpoint anymore and the program doesn't stop there. The only way to remove it (as far as I know) is to delete the character and retype it.

Apart from that btw, this is the best brainfuck compiler/interpreter/debugger I've ever seen, thanks a lot for making it :).