The Book of Blood: Chapter Two: The Perdi - S2-E6
Plot hole: When announcing the 14 deaths, they make a generic statement to the friends and family of everyone in the pods, without first telling the affected families directly?! There's no way this would be dealt with like that - not least as they all then seem shocked that the parents start a riot/panic about whether their children are dead or not. Anyone with half a brain cell would have seen that coming a mile off. Not to mention that later on we discover one of the parents STILL hasn't been told if his daughter's alive or not. If this was a coverup or otherwise secret they wouldn't have said anything - there's no reason to announce the deaths but not clarify who died.
Mondays Are for Murder - S2-E13
Plot hole: In an effort to keep Glenn's death as quiet as possible, Higgins hires a private pathologist to do an autopsy to see if there were any foreign substances or poisons in his system when he died. A few scenes later it is revealed that Glen was undergoing chemotherapy. How is it possible that the pathologist missed the cancer and the chemo treatment in his investigation? What he found was an excess of antacids.
Plot hole: Cadmus sets a brain-controlled Connor loose in public, without apparently remotely considering the possibility that anything might go wrong. When he regains control all they've got is a few goons onsite armed with regular ammunition - what did they think that would achieve? They know exactly what he's capable of. Either have kryptonite ammo or don't bother having anyone there at all.
Plot hole: At the end of the previous episode, Ms. Haman is shot by a Japanese soldier. The shot is severe enough to make her collapse to the ground and fall unconscious. But in this episode, she appears perfectly fine without any sign of being shot, and without any injury in sight. (00:07:30)