I don't know if it's a flagrant 2 but it's probably, at least, a flagrant 1. Especially if you watch it from the overheard angle, you can see really clearly that Melo is not jumping toward the basket at all, he's jumping into Nurkic on purpose. That's not uncommon (IT and Harden and many others have made a career of it) but rather than turn his body away from Nurkic, toward the rim (as one would do when one is trying to score) he actually turns his body away from the basket.
To the ref's point, it does look pretty unnatural to me.