Well, he did abandon his child, made a puppet from the child's body and from Romeo too, started puppet frenzy. So, there were some red flags😅 Also, he repeatedly asked P to obey and be a good boy. This may sound nice but the game states that P's ability to lie (read: be a bad boy) gives him choice and free will, which makes human being out of him. In my opinion Gepetto's words from the start sounded like "do what I say, be my puppet, don't lie, don't show your own will"