Yeah I can see that point. I will add some hint in the quest description.
The slime one probaly is a bug. You can upgrade the ability to cost less but for some reason the game probaly thinks you already got the first upgrade. Did that happened everywhere or just at certain spot?
Yes, original was intended that fleeing from a Mimic makes them they remained open after they got discovered. After all they can't fool one again.
The other one sounds like a bug. You did not get a game over there or what happened?