Plot hole: Those people created for medical experiments cannot run. In fact they can barely walk, so how come they can climb nearly as fast as Rose? What's more, when you see them climbing, they seem to have little ability to coordinate hand over hand. Even with the delay brought on by the cat-woman-thing, they should not have been able to keep up with her.
Be Afraid of the Dark (2) - S3-E12
Plot hole: When the Corrodium Beam is shut down, there is a brief scene of the sky clearing at Mount Rushmore. But on the cliff face all four heads are seen, whereas the head of Theodore Roosevelt got crumbled in "Secrets," and it's too far forward to have been carved into the mountain face, in place (and same position) of the old head, yet again.
Recognition - S1-E17
Plot hole: Bridge could have used his powers to figure out if Wootox and Sky's bodies were still switched.