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.
Episode #5.2 - S5-E2
Plot hole: Collision between the two planes would have been prevented by TCAS (traffic collision avoidance system) computer systems installed on both planes. The TCAS systems automatically coordinate with each other and issue a TA (Traffic Advisory) with an audible "TRAFFIC, TRAFFIC", then if on a course that could result in a collision or near miss, issue an RA (Resolution Advisory) to their respective flight crews. Typically one plane's flight crew is audibly ordered to "DESCEND, DESCEND" by its' TCAS and the other plane will be instructed to "CLIMB, CLIMB" by its' TCAS. The flight crew is required to follow their TCAS instructions over the air traffic controller's. All commercial airliners are required to have a functioning TCAS computer. These systems were obviously not under control of the terrorists, they were conveniently ignored in the plot. (00:03:20 - 00:06:47)