Plot hole: In the pilot Jimmy finds out Lucy is pregnant while visiting her cell. In S2 E21 (Inside Probe) he finds out while taking to Lucy on the prison phone.
Plot hole: In Russia, Soldier Boy is shown heading to the airport, He wanted to get to the US and start his revenge against his team. Problem is: he has no documentation and money to take a flight. Even if he stole the money somewhere, still would be impossible to travel without the proper documents.
Plot hole: The bad guy somehow knows what is going to happen (via the sketches) even though the events haven't happened yet, like knowing Mrs Peel was going to show up at Pool's mansion in that catsuit and hat, and that the scenes were going to play out like the sketches.
Plot hole: Someone as careful and controlling as Timo would never force anyone into working for him, for exactly this reason.
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: 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: As the first prisoner is being pulled towards the organ cutter, you see on the wall the exact shape of the body organs for the brain, lungs, heart, liver, stomach, kidneys and testicles/ovaries that serve as guides and a track for tiny saw blades to come out and cut into the person's body to harvest these organs. The problem is these are in a fixed position, which might work for some people. However people are different sizes, shapes, and heights and most wouldn't match up to these blade guides. So a good majority of the people they cut apart to harvest organs out of wouldn't even give them good ones as the blades would cut into the organs and ruin them. (00:25:20)