Continuity mistake: When Dex stabs Lila, the knife goes in near her stomach, where her vest starts. But in the close up shot, the knife is higher up in her, in her chest. (00:48:45)
Continuity mistake: In Paris, when Dexter grabs the knife off the table in the close-up, he's wearing the black glove on his right hand, but it cuts to the wide shot and both of Dexter's hands are bare; then in the next shot the black gloves reappear. It's rather odd that the actor was even filmed without wearing his gloves in the wide shot.
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.