Factual error: In the police report Dexter examines, Emmett Meridian's name is followed by PhD, and yet he is referred to as a psychiatrist and prescribes medication. A psychiatrist would have an MD after his name, and a psychologist (PhD) cannot legally prescribe meds.
Plot hole: If we assume that Dexter took off the oil cap while it was still in the shop for Arthur, it still doesn't explain how Dexter got the jump on him when his car (hours later) broke down. Arthur's not shown to stop, but to merely drive for hours on end until night. Arthur's on a barren strip of road with no other cars or traffic to be seen for miles. It cuts from Arthur looking in his engine to Dexter suddenly walking out from behind the Mustang. The only explanation is that Dexter waited in the car with Arthur, which doesn't make very much sense. All this takes place in the last 15 minutes of the finale.
Character mistake: Louis Greene, Masuka's new intern, is asked to find the person who purchased Rudy's prosthetic hand. He is unable to do so; however, as a consolation, he says "I installed a modded-up Intel chip to overclock your CPU." You can overclock your CPU, but you don't need another chip to do so. (00:44:00)
Other mistake: Doaks says he saw the man's gun and chased him, lots of questions arise about what happened, but no-one mentions how a cop has no right to ask a person about a gun they have on them without probable cause. Doaks has no reason to even go after the guy.
Continuity mistake: The bathtub Rita is found deceased in is a standalone without a shower door, unlike previous episodes featuring the bathroom with a shower/tub with a sliding door. In a previous episode, Rita refers to the home as a "one-bathroom" house so it's not possible this was intended to be a second bathroom.
Continuity mistake: In the shot where Angel gives Dexter a gift from the recently deceased Maria's office, we see Masuka through the window in front of Dexter. Masuka then enters Dexter's office, showing Masuka in two places at once for at least two seconds. (00:30:55)