When Dexter first meets Cassie in "Scar Tissue", she greets him by saying, "You must be Dexter...I'm Cassie, 4B." When she's inside her apartment toward the end, it has 8B on the door, just to the right of Batista's hat.
The end wall in Cassie's apartment should be solid as it is a shared wall with to Dexter's apartment, yet from the inside there are windows.
When Zach goes to Dexter's place at night, Dexter emphatically states that he never do it again and they can't be seen together. Later on in the show, after Zach leaves the police station during broad daylight, Dexter is waiting for him in the station parking lot and they sit and talk. That makes no sense.
In the finale of the previous season, Hannah escaped police custody while at the hospital. Before the scene where Dexter kills LaGuerta, Hannah is seen dropping off an all black plant in front of Dexter's apartment, which SHOULD have alerted Dexter (or at the very least Jaime) that she was free and had been there. Even before this, hospital personnel should have alerted Miami Metro (especially Debra) to Hannah's escape and a BOLO should have been issued. It took seven episodes of the final season for anyone to realize that Hannah was on the loose, and yet the mysterious black plant has never been found or spoken about.
Dexter tells Dr. Vogel he didn't kill until he was 19, however when Debra first found out his secret and asked how long he's been killing he told her since he was 20.
Zach goes to Dexter's apartment and continually knocks on his door when Cassie comes out of her apartment to say that it looks like he's not home. There is no apartment number seen on her door as she's coming out, nor when she returns back inside, but 8B later appears on the door when Miami Metro is called to the crime scene at her apartment.
Dexter says he's in Kendall but the semi-arid, industrial landscape behind him looks nothing ends remotely like Kendall, which is a middle-upper class suburban neighborhood characterized by ranch-style homes and lush green vegetation.
It makes no sense for Dexter in the phone call at the beginning to not tell Deb she has been sedated by Hannah. They have been attacked by a known murderer for some unknown purpose, both their lives are possibly in danger and that kind of information is crucial.
There is no way for Hannah and Miles to have a big noisy physical fight where one of them stabs the other to death on a yacht that size without any of the crew noticing.
It makes no sense for Dexter to tail Hannah and her new super rich husband in the open, with no GPS tracker, in his personal car that she knows, after she has attacked him and Deb and is therefore bound to expect something from him. It is inconceivable she would not make him, leading to all kinds of trouble for Dexter. He might as well drive right up to her to talk.