I've also noticed this happens with explosions, bombing rocks to create gaps, and sometimes even after boss fights (this seems to be particularly bad with Reap Creep).
For anything that requires creating explosions/blowing up rocks over gaps... I generally just keep the console on and give myself a Hanged Man card if I need a workaround. Temporarily giving yourself the Dogma item too will give you flight that even works in the Mines II chase sequence (because it's a plot item and cannot be erased).
In the instance that I can't get past a boss, I'll generally just use the console to create a Ehwaz to get down to the next floor. It stinks to have to use the console, but it's better than not being able to progress because the game keeps crashing...