Well, lots of things. The thing that most annoys me is SFMAs that use Fire Farm NPCs. Your average non Fire Farmer isn't built to take that much fire damage so it's a PITA when you run into mobs and mobs of them.
On a more comedic note, when I was writing my first AE arc (Dark Deeds in Galaxy City: Part One), I had given one mob of enemies Beam Rifle and Force Field. A beautiful combo you'd think. Ah, not so fast! Myself and my two test mates ran it and we were bounced around the room with Repulsion, could barely land a hit on anything and eventually PINNED TO THE CEILING AND BEAM RIFLED TO DEATH.
So.
Force Field was swapped out for Time Manipulation. Yeah, layered Distortion Fields can SLOW things down, but it was better than the test version! Be thankful none of you ever saw it.