Yeah, that's a known problem. I think you need to start a new run and try to finish off the enemies faster because the game just works like that for some reason
Myeaaah, sorry. What I said is the only solution to the problem I know. This game is really not well stitched together and there will sadly be no fix to this issue
You know what they say - if you can't beat it, turn it into a feature.
In this case, I think it would be that once you defeat that red tentacle guy at the end, the game automatically resets with a higher difficulty, sending you to a new "level" and restoring the spawn rates of the others.
