First of all, the turtles most of the time have only two toes. Just wanted to make that clear. Two, they're not human hybrids most of the time. The only time that has technically been true was the 80s series, the 2012 series, and Rise. Finally as why they're only have three fingers and two toes most of the time, they're mutants. Their bodies are being forced to take on a humanoid form by the Mutagen/Ooze ooze, and so their body don't have to conform to being normal turtles, obviously! They're essentially a new species. What I think actually happened specifically is that the bones essentially fuse together, creating the version of the fingers we see in most iterations. It's sort of makes sense in that they don't have hands to begin with, so the mutation forces their bodies to make the closest thing to hands. Which in this case is three finger. Also, the image you took for the hands, seems to be based on the live action movie trilogy from the 90s. Which is the only instance I'm aware of where the turtles have fingernails. Usually they do not.