
Getting Even - S4-E3
Plot hole: At the end of the episode, having conned Veronica Powell out of £600,000 - the purchase price of the house and contents they sold her - Danny taunts her by telling her that they did nothing wrong, implying that she has no legal recourse to recovering her money. He's wrong. One of the gang, Billy Bond, bids against her in the auction for the house, boosting her bid from £220,000 to her final offer of £600,000. Bond has no money and no access to any, and no assets that could be realised to cover the bids he made, something that would be easy for a lawyer to prove. It's called shill bidding and it is very illegal indeed. Since Bond and Ash Morgan (who gave Powell false information during the auction, spurring her on to bid against Bond) are both standing next to Danny when he makes his announcement I find it hard to believe that a shrewd, hard-hearted businesswoman like her would not realise that she had been conned and would not get her lawyers and the police on the case on the spot.

Mr. Monk Goes to Jail - S2-E16
Plot hole: It is unrealistic that a prison cook who did not punch out would not be missed or found until the next day, especially after a lock-down scenario as portrayed in this episode, where a meal has been poisoned - likely in that very kitchen.

Under & Out - S3-E11
Plot hole: Gretchen, Lincoln, and Sophia were able to visit Scofield and Whistler in Sona without Gretchen being recognized. She was taken in for questioning in episode 9, but she managed to escape and kill General Zavala and one other guard. The other guards knew that she was the one who killed Zavala but she was still able to sign in for visitation.
gordy16
Plot hole: In this episode, the Duboises make such a big deal about Ariel being old enough to finally learn to drive. However, two episodes previously ("Things to Do in Phoenix When You're Dead") Ariel drove to school with Joe, and Joe complimented her on her prowess.

Plot hole: At the end of this episode Red takes off his shirt revealing his burned back, which leaves us to think that he might be Elizabeth's dad. However, this particular mark should have been noticed and written down in Red's prisoner file when he was taken into custody the first time (Episode 1). In that case Elizabeth would already know that Red is burned and could have asked some questions about it.

Guy Walks Into a Psychiatrist's Office - S2-E1
Plot hole: In this episode Tony tells Janice that he has just put their mother's house on the market. In season one, the house had already been sold.
pinkwafer
Plot hole: Columbo is in the Pauley's hotel room trying to figure out how the bottle landed upright next to his body after he was shot. Devlin - the murderer - turns up unannounced and uninvited. How did Devlin explain that he knew where the victim was staying when he was murdered? Media reports might have mentioned the name of the hotel but there is no way they would have included the room number.

Plot hole: A central plot device in this episode is that there is no six letter word made up of the letters EXVIN, so the murdered man cheats at the word game by playing a word he knew to be inadmissible - exvin, a wine connoisseur who no longer drinks. Since he is supposed to be a stone cold killer player at this word game, don't you think he would have thought of Vixen? Sara Sidle points that word out later - why wouldn't a world champion word game player have figured it out, using a safe, common word and avoiding a possible challenge?

Dead Freight - S5-E5
Plot hole: Preparing to steal methylamine from the train, Walt, Jesse and Mike measure off a predetermined distance from the railroad crossing, which happens to coincide with a handy arroyo, where they bury their tanks. Problem is that they couldn't have known that distance (calculated by knowing the position of the methylamine tanker car in the train) until Lydia told them. But she didn't call that info in until the night after they'd already buried the tanks.
RattletrapSuggested correction: They were counting on the tankers being at the back of the train, far enough away and at a curved angle so that the conductors wouldn't see them, and the hoses they were using would have been long enough to reach the tankers on either side of the one they stole from. Their heist hinged on a lot of educated guesses and luck, especially because they would have had to abort if the tanker was at the front of the train, but being lucky doesn't make it a plot hole.
Phaneron

Day 2: 7:00 A.M.-8:00 A.M. - S2-E24
Plot hole: Peter Kingsley is shot and killed by a man in a helicopter just as he is about to kill Jack. Kingsley would definitely have heard the helicopter approaching.

Surf's Up! Joker's Under! - S3-E10
Plot hole: An amazingly precognizant Dick Grayson is already wearing his surfing togs before Commissioner Gordon calls to say that Joker has invaded the surfing community. (00:04:30)
Jean G
Plot hole: After Sabrina and Tarloff have finished their rehearsal, Kris is able to pick the real sword with no hesitation. There are still six swords left in the basket (one is real, five are fake). They all look the same, so how could Kris know the exact position of the real one? (00:43:30)
Great_Captain
Plot hole: It turns out in the climax of the episode that there are no bullets left in the gun and Miss Fisher knew it. That would mean then that she deliberately wasted minutes with Simon bleeding out on the floor when Chaim was holding them at gunpoint with an empty revolver, for no discernible purpose.
Sammo

After Hours - S5-E8
Plot hole: Beckett and Castle lose their cell phones and wallets and are being chased by the mob. Beckett steals a cell phone from a car but can't use it, since it is locked and then shut off remotely. Any cell phone can always dial 911, whether locked or blocked from service.
Grumpy Scot
The Man in the Fallout Shelter - S1-E9
Plot hole: At first the victim (Careful Lionel) is described as not returning to pick up his new shirt in November 1958, and possessing love letters dated from 1957 through early winter (November) 1958. Booth reports the fallout shelter where Lionel's body was discovered was sealed in 1958. Later Lionel is described as reported missing by his boss in January 1960, and the illegitimate child he fathered was born in 1960 as well. That would mean his boss didn't notice he was gone for over a year, and his pregnant girlfriend was with child for at least 14 months.

Plot hole: The CSIs catch a murder suspect putting down a drink can when reviewing security footage of a robbery, and immediately realise they didn't see it at the scene so assume one of the first cops on the scene must have removed it. Thing is though, the murderers shot out the security camera before the actual shooting occurred, meaning there was loads of time off-camera for the killers to take the can with them, but the CSIs never even consider this - they jump to the conclusion a cop took it even though there's no actual evidence for that.
Jon Sandys

Plot hole: They only take out the shrapnel from the gut shot - they never deal with the shrapnel in his shoulder at all. (00:04:25 - 00:05:00)