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.
The Night of the Raven - S2-E3
Plot hole: Antoinette is making miniature clothes for the soon-to-be shrunken West, but when West drinks the antidote to make him normal-sized, he is wearing the same clothes which would have been shredded as he grew back to normal size.
Plot hole: Tom discovers Claire's body in the wardrobe of his motel room. He leaves the room, and within a minute returns to the room, accompanied by the police. The body has vanished from the wardrobe, but given how little time Tom was away from the room, it is impossible for someone to have moved it, particularly given the weight of a corpse.
The Spores - S2-E7
Plot hole: Hal and Roy could not open the spore case with an electric power drill, but later a married couple pops it open with a hammer and chisel, then much later some children acquire the case and easily open it.
Plot hole: As the first prisoner is being pulled towards the organ cutter, you see on the wall the exact shape of the body organs for the brain, lungs, heart, liver, stomach, kidneys and testicles/ovaries that serve as guides and a track for tiny saw blades to come out and cut into the person's body to harvest these organs. The problem is these are in a fixed position, which might work for some people. However people are different sizes, shapes, and heights and most wouldn't match up to these blade guides. So a good majority of the people they cut apart to harvest organs out of wouldn't even give them good ones as the blades would cut into the organs and ruin them. (00:25:20)
Recognition - S1-E17
Plot hole: Bridge could have used his powers to figure out if Wootox and Sky's bodies were still switched.