Plot hole: The FBI is looking for a "very tall" guy who has been identified as such by various witnesses and by their own expert due to the entry angle of a fatal bullet wound - 6'5" at least. They send Elena into a bar near the end of the show to meet the Albanian perp who when he arrives is barely average height.
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.
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.
Grass on the Streets and Weeds on the Rooftops - S4-E10
Plot hole: Beth surprises Jamie in the act of disposing of his father's body at the train station. But Beth doesn't learn about the train station until season 5, episode 8. So, how did she know where to catch Jamie in the act?
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)