Revealing mistake: When Dexter stomps on Barry's kidney, you can see his foot doesn't even make contact with Barry's body.
Revealing mistake: When Dexter is fighting Liddy, in the van after kidnapping Dexter, the knife is a rubber fake knife. (00:38:15)
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.