What if transforming into the Obscurus is kind of like the Hulk, it happens whenever Credence is feeling anything really intense. Graves (don't care which as long as it's a Colin Farrell's face) is fucking Credence for the first time and the dick is so good It makes him start turning into a cloud of black smoke.
Credence/Graves, transforming into the Obscurus doesn't just happen when Credence is upset