Plot hole: It turns out that the Venus Fly Trap ate Dr. Collosso, but this doesn't make sense for a few reasons. 1. There's no way that it could've opened the kennel without completely destroying the door. 2. The shot was off it for only 3 seconds, it couldn't have eaten him in that amount of time.
Plot hole: Amy lets Scully place the witch in the break-room, but how could she have known that after captain Holt steals the crown out of the locker, he would go there? And not for example goes back through the window he came from.
The Marathon - S4-E3
Plot hole: Jason cheated in three different ways in order to beat Aurelius in The Marathon, and admitted it. So the bet that they made between them is null and void. But the last shot shows them living up to the terms, which includes Aurelius starting to eat his own shit (literally), so revolted that he's trembling. Apparently the writers really really wanted to include coprophagy. But who would eat faeces for a bet, if you can simply avoid it by reminding your opponent that he cheated? Or even better, many would say that cheating means losing automatically, so he's the one who should be eating his own shit.