This is kind of a reflection of all those amazing fics where Grindel has been treating a captive Graves as an animal and Graves has kind of broken as a result. No one quite knows how to treat him so they call in everyone's favourite magizoologist and Newt manages to get him calmed down. Everyone's over the moon with this and leaves Graves in Newts care entirely.

Newt has no idea how to deal with a traumatised person but he's excellent with creatures so he goes with that and Graves just responds as an animal. Newt is thrilled, here is a person finally acting in a way he can understand. Everyone else is just pleased that Graves is calmer and being looked after now, since no one expected him to recover from that level of abuse anyway. There's just enough of Graves left in the back of his mind to protest that he's a man not a pet but then Master touches him and everything is perfect again.

Your choice on whether Newt is doing it on purpose or if he doesn't realise that he's carrying on on Grindels abuse.