Visible crew/equipment: When they are at the crime scene, you can plainly see the camera and camera man reflected in Special Agent Lundy's sunglasses several times. When it is a close up shot, it is even more obvious.
Revealing mistake: When Deb is texting "Looks like it" to Anton, the buttons she presses on the keypad do not correlate with the message itself and the phone doesn't show any auto-correct feature being utilized, indicating that the text message was added in post production.
Other mistake: An extra is walking in the background with a measurement wheel while Debra is talking with Lundy outside of the warehouse. The character is hovering the wheel over the ground and not actually using it for its intended purpose. (00:17:10)
Answer: No, Harry is not the real father. While he did have an affair with Dexter's biological mother (Laura Moser), this was when she was his C.I. Dexter was already born at that point.