The car that Arthur Mitchell drives away in is a vintage Ford Mustang, but the car that Jonah Mitchell was driving earlier was a vintage Shelby Mustang GT500.
After Dexter shoves Quinn to the pavement he is seen speeding away in his SUV with the license plate L3S537. Dexter pursues Arthur to the Stafford Bank with this plate visible in the chase. The person whose car Dexter hit damaging the rear-view mirror would have reported license plate L3S537 meaning the police would be looking for a vehicle other than Dexter's. Once at the Stafford Bank Dexter's license plate is back to the OBN091.
As Dexter attempts to catch Arthur Mitchell, he pulls up beside the "Stafford Bank" car parking structure. In shots when he is walking up to the car park the "Stafford Bank" sign that had been previously visible above the car park entrance/exit has gone, revealing the real-life signage, "Public Parking".
Towards the end, as Dexter is found in the garage by the raiding police he is speaking with Deb and his shirt collar is up on the left side and in the next scene it is down and then up and in the next scene and finally it is down again.
Previously, when Dexter and Arthur were in the garage and Dexter discovered the coffin that Arthur built, it was stored in a rack with four shelves with the bottom shelf about 4 inches above the top of the coffin.
During the raid, the rack is shown to now only have three shelves. The bottom shelf has been taken out to make room to open the coffin lid. Also there are completely different items on the shelves.
The close-up of the car in from of the Miami Metro police station shows a Florida license plate on the front of the car. Florida does not have front license plates, only rear ones.
Deb should be on suspension after the Christine Hill suicide debacle, as should Quinn and their superior. Deb recklessly met the murder suspect alone in her own home. Her partner let her walk into that meeting alone while he waited in the parking lot instead of backing her up. Their superior shares responsibility because he/she either signed off on this blatant violation of standard procedure or tolerated the departmental culture that led to it.
On the Trinity Killer victim chart in the Miami Metro Police Dept., the 1995 victims are listed on the chart as being from "BILOXE". This spelling error of Biloxi, Mississippi is clearly visible while Batista is talking to the group (at around 18 mins).
When Dexter is in the Trinity's garage, he sees the Mustang's broken windshield and realizes that the vintage Mustang is gone. However, that windshield is obviously from the modern and not vintage car (due to the dotting and shading on the edges AND because of the shape of the windshield itself) and broken surface does not correspond to the broken surface on the Mustang's glass.
After Arthur Mitchell leaves the police station, Dexter rushes to catch up with him, as Arthur leaves the building, you can see Dexter's blue shirt through the glass, waiting in the entrance way for his cue to rush outside and chase after him.
A reflection of the crew's crane can be seen on the side of Arthur's Mustang as he is driving away from the body shop.
In the wide shot of the Miami Metro police station, the viewer can see mountains in the background. There are no mountains within 600 miles of Miami.
No explanation is provided as to why Dexter didn't just use Arthur's van to drive away from the parking garage and murder/dispose of Arthur (now that he finally has him at his mercy) before going back to deal with the damage he caused.