Mr. Monk and the Astronaut - S4-E14
Plot hole: There is no drug in the world that could render a healthy adult unconscious for two days with a single dose, but let's go with the dramatic licence and allow that there is. Any such drug would be instantly detectable in any one of a dozen toxin screens carried out during an autopsy, and isn't someone going to wonder how a comatose woman hanged herself?
Plot hole: At The Beginning Sam stated that the missing teacher comes to work by subway every day. But in the flashback of his conversation with the drug dealer, he's about to get into his car. (00:13:00)
High Octane - S5-E7
Plot hole: When Dex is doing the jack in the box ,he is hanging out the sun roof driving with his feet, using the cruise control. When he is decapitated, the body falls and the car spins out and stops. The car's cruise control was still on. The car should have kept going until the brake was pressed. Even if the body hit the brake on the way down, it would have coasted to a stop and not spun out and screeched to a stop.
Here There Be Monsters - S1-E10
Plot hole: The female police officer has a theory that Johnny was the Strangler in the case the papers claimed he helped solve but this hardly makes sense. If she was researching him as was seen in the episode, surely it would have said something about Johnny being in a coma during the bulk of the murders since the story was about Johnny.
A Scooby-Doo Valentine - S3-E3
Plot hole: It's never explained how JC Chasez and the Hollywood extras impersonating the gang gained the super strength they possessed to do things like ripping car roofs open or holding up the Mystery Machine.