Plot hole: Why would Danger Mouse go on the roller coaster at the end without seeing Greenback go on it first? Greenback went first in the ghost train. It also doesn't make sense that Danger Mouse would go on it when Penfold pretty much tells him flat out that it IS a trap.
Plot hole: Gripper, Woody, and Randir are suspended from school for two weeks after their involvement in the fight. Woody and Randir appear in the next episode, but Gripper doesn't return until episode 14.
Into the Mouth of Evil - S2-E23
Plot hole: While fleeing the guru's disciples through a narrow side street, Jackie gets cut off by the van driven by Dr. Jamba and associates, stun-sprayed in the face, and then loaded into the van. But with three brutish-looking guys being so close to their quarry, the real crooks can take the time for dragging Jackie around to the back door instead of loading him through the side doors?
The Muh-Muh-Muh-Murder - S1-E25
Plot hole: Daffy isn't able to escape Porky's house until he gets the keys, but later it is revealed that the reason he couldn't get out was because he was too weak to open the door. If that was the case, the keys shouldn't have been able to help him get out.
Plot hole: During Ryder's report, as Bruce and company watch it on TV, the camera suddenly zooms in on Joker standing on a catwalk above Ryder, and none of the crew, especially not the camera man who caught the villain, makes a comment about this. They may have thought the Joker (or rather an impersonator) was perhaps a surprise gag in the show, but since this is supposed to be a serious documentary report, it is still strange that they wouldn't point it out.