During the fight between Zoe and Dexter she throws his cup at him; that cup hits a wall and breaks. When Dexter is cleaning up the cup is near the middle of the floor, with none of the pieces any where near a wall.
After Dexter finishes fixing the garbage disposal in his next victim's house, he is knelt down and is taking his gloves off. The cupboard doors behind him are open. Then when he is given a hand up he is no longer holding his gloves and the cupboard doors are now magically closed.
When Dexter removes the trap under the kitchen sink to check the garbage disposal for the missing rubber gloves, there was absolutely no water in the trap at all.
When the Trinity killer "accidentally" bumps in to Lundy you can see the camera man in Lundy's sunglasses several times.
When Dexter mentions that Zoe Kruger is trying to flee to the Philippines, he states that they don't extradite to the US. The Philippines and the US have had an extradition treaty since 1996.