Plot hole: At the end, all the things and beings that manifested from paintings or drawings are pulled back into their paintings or drawings, including K-9 from Clyde's book. But in the last scene in the Vaults, the puzzle lock can be seen still attached to the Abomination's case, even though it was manifested from a drawing in Clyde's book. The crew probably forgot to remove it after the scene where the paintings went back.
Other mistake: Mr. Smith scans the Mona Lisa and determines that it is genuine from DaVinci's brush strokes. He should have also noticed the words "This is a fake" written in felt tip under the paint, from when The Doctor replaced the Mona Lisa with one of DaVinci's "forgeries" in "City of Death."Captain Defenestrator