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.
The Night of the Tottering Tontine - S2-E16
Plot hole: They said they couldn't leave the room because the door wouldn't open and then they all went to their rooms. How did they get out?
The Night of the Deadly Blossom - S2-E25
Plot hole: There are two rockets to be launched. The right rocket launches. It is important for the plot for the remaining rocket to explode without being launched. Without explanation, the left rocket just falls off its ramp, lands on the floor and shortly explodes. (00:46:10)