Continuity mistake: Arthur and Dexter make a u-turn to avoid a DNA checkpoint. The view from outside the van shows no oncoming traffic, but the view from inside the van shows several cars waiting for them to complete the u-turn. (00:53:20)
Continuity mistake: When Dexter is packing kill tools for the road he "packs light" and chooses a knife and hammer. However once he's at the hotel room setting up the kill room he unrolls his entire set of tools like he does at all the other murder room scenes.
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.