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.
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.
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.
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: 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.
Plot hole: At the start, they state that they have 96 criminals to go. They bring up the photos of all 96 wanted felons. They then learn that Machado has been pushed to the top of the list and they bring up his file. You can see his mug shot on the screen, among the list of 96, as they zoom into his file. If he is in jail and has not yet escaped, how can he be in the list of 96?
Plot hole: If Andy really did enlist into the Army Reserves and "forgot about it" like he claimed a warrant for his arrest for desertion would have been issued, which the police would have seen when he was arrested for pot possession in the episode "Lude Awakening." After seeing the warrant, the police would have called the Army, and he would have been returned to military control to face desertion charges. He would not have been released and sent a letter a few weeks later simply telling him to report for duty or face military prison; the option to report for duty would have no longer been available when he was gone long enough to get put in deserter status.