So it's not exactly about enemies dying at the same time that is the problem, it's more of a bug/glitch that's happening.
So basically, enemies have like a one in five chance of dropping a "Gem", in my game I have an AOE (Area of effect) weapon, and if it kills one enemy that were supposed to drop a gem, all of the enemies killed at the same time will drop gems.
How can I prevent this? I was thinking maybe destroying enemies at not the same time would help (hence the title), but I'm up for other suggestions!