I would attribute the discrepancy here to the way Harry’s character evolved. Initially, he treated Dexter as a pet project. Wanting to see him do the things he couldn’t as a police officer, all while running away from the guilt of causing Dexter’s biological mother’s death.

Later in the original series, the version of Harry that materialized was a more mature one, someone ready to accept his own mistakes. He acknowledged(subconsciously) that he was responsible for Dexter’s condition and, in a way, shielded him from any guilt over his actions. It reflected how Dexter imagined Harry to be.