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 FBI is looking for a "very tall" guy who has been identified as such by various witnesses and by their own expert due to the entry angle of a fatal bullet wound - 6'5" at least. They send Elena into a bar near the end of the show to meet the Albanian perp who when he arrives is barely average height.
Plot hole: Parker gains access to the external room using a valid security card, they figure out the CEO's passcode which opens the burn room door...and yet the room inside is still protected by a swarm of lasers. Was the CEO supposed to dance through the laser sensors like Parker does every time he goes in?
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.
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.
Plot hole: When the two henchmen who break into Nick's loft to kill Lisa are captured, the case is closed. But the two thugs were reporting back to a boss who wasn't caught, and who surely would have sent more hitmen after Lisa. So the case shouldn't have been closed.
Plot hole: When Wilson does an ultrasound to check for cancer in Alex' ovaries he fails to notice the fact that she doesn't have a uterus. If he mistook her bladder for her uterus, which sometimes happens, she would have appeared to be missing her bladder instead. Yet Wilson doesn't pick up on anything being missing.
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)
Plot hole: Vaughan discovers Lauren is a mole when he goes through her briefcase and discovers the wig, gun and fake passport she used in Germany a few hours before - surely even the worst secret agent in the world would have enough sense to get rid of such incriminating evidence as soon as possible, and not carry it back to the USA (sneaking it onto a plane, presumably) and leaving it in the room where the man you're lying to sleeps. Lauren is a highly skilled agent, if the Covenant selected her for a mission this important, so it's out of character (without an explanation) for her to be so sloppy.
Plot hole: Laura successfully knocks out both bad guys, steals their van and crashes through the warehouse doors. The van doesn't stall, but inexplicably, she stops it, gets out and runs away on foot, even though the baddies are coming to and coming after her. Not the option you'd expect a kidnap victim to choose: most people would floor it and keep on driving. (00:23:40)
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.
Orpheus in the Undergrowth - S2-E2
Plot hole: When Jeremy stopped to drink his water, which turned out to be vodka and which killed him via a heart attack, why did he hide himself away, surrounded by plants and only found by his mobile ringing? And why would he put the lid back on the bottle in the throes of a heart attack?
In Too Deep - S5-E8
Plot hole: Carter is apparently just learning about Feynman's Day, which Allison explains as "Eureka's version of April Fool's Day." It's highly improbable that Carter could have lived in Eureka for five years and still be oblivious of this, especially given all of the hijinks that happen.
Plot hole: The pictures James took were developed from his camera into photos even though he was arrested while taking those. How did they get developed? James' father didn't approve and his mother said she had found that stack of photos after the police searched his room. (00:26:30 - 00:30:00)
Episode #1.5 - S1-E5
Plot hole: Leon Hamilton is the most hated man in Sainte Marie, with over 900 people on the island conned by him. Yet exactly one person in the whole island knows how he looks like, every newspaper and website never ever published a picture of him even during the very public trial when they were trying to get their thousands of dollars back nor publish an archive picture after his death.
The Inspired - S9-E2
Plot hole: At the beginning of the episode, PD let the suspect go (twin 1) because they accidentally arrested him for the crimes that his twin brother (twin 2) committed. Hotchner still wants to question twin 1, but a lawyer threatens Hotchner to not go near the wrongfully accused twin 1. However, in the previous episode, FBI and cops pursued twin 1 and twin 1 didn't pull over. It would be legal for twin 1 to be detained on a reckless driving or eluding the police charge.
Plot hole: The car was tracked down by finding the original car key on Jimmy's body. If he had stolen the car from the original owner, how did he come to have the original car key?
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.
Plot hole: In episode 1-7: "Unraveling," Christina and Jesse get on a bus to New Haven, first thing in the morning. Christina left the Kramers's house before breakfast. Then, they ride on the bus all day until getting trapped in a terrible storm in the dark of night. But New Haven, CT, is less than a seven hour bus ride from the Jersey shore, so anything that happened to them on the way there should have been in full daylight.