Stupidity: Dexter's decision not to kill Trinity when he had the chance eventually led to Rita's death, a mistake Dexter told Deb he would never make again. However, at the end of this episode, he decides to spare Oliver Saxon so Deb can arrest him. Dexter doesn't stay to ensure that Deb successfully has Saxon in custody, which leads to Saxon escaping his shackles with the unwitting help of Deputy Marshal Clayton, and shooting Deb before leaving the scene. Dexter therefore does make the same mistake again.
Stupidity: After Dexter tells Hannah that the U.S. Marshals have distributed her picture everywhere, she questions how she will be able to flee Miami for Argentina. Dexter reasons he and Harrison can leave with her because the authorities won't be looking for a woman traveling with her "husband and child." It doesn't matter who she is or isn't traveling with. If the authorities have shared her picture, she's going to be flagged when she goes through security at the airport, which Dexter should certainly know. This is made all the more egregious when she takes Harrison to the hospital later in the episode and is ID'd by the receptionist.
Stupidity: Hannah spends the entirety of season 8 as a fugitive in hiding, but never thinks to make herself less conspicuous, such as dyeing or cutting her hair, or wearing disguises when she goes out in public.
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.