Producer David Heyman says the scene was taken out because they didn’t want audiences to know exactly where the next movie was heading. But then he went ahead and told everyone about what happened in the scene anyway.
The climax oof Fantastic Beasts and Where to Find Them centers on the reveal that Credence Barebone (Ezra Miller) is the source of the Obscurus. the dark cloud creature that’s flying around New York and leaving destruction in its wake. His sister, Modesty (Faith Wood-Blagrove), was a red herring the whole time and wasn’t an Obscurial at all (Obscurials being the name for the witches and wizards hosting an Obscurus).
Eventually, Credence is tracked down, and he’s such a danger that the American Aurors kill him. And that would be that... except the Aurors do this while Credence is in his incorporeal Obscurus form. Sure, the circumstances are enough to give audiences a little doubt about the truth of Credence’s death, but it’s ambiguous at best.
Or it would be if producer David Heyman hadn’t spilled the beans to Cinema Blend. He flat-out said that Newt was less important to the movies than Grindelwald and Credence going forward. And he said that the film originally had a scene where Credence’s survival was shown to the audience:
We actually had a scene, which we cut, which was Credence going to a boat, to get on a boat somewhere else. But we cut that, because we didn’t want to have it be such an, ‘Ahhh, here we go.’
So, what was that scene kind of like?
Him getting on a boat, maybe a boat with Newt, maybe not, and heading off out of New York.
The filmmakers didn’t want it to be an “Ahhh, here we go,” but Heyman just decided to describe the scene to everyone? Okay. Maybe they just didn’t want to set up the sequel so obviously, and let this first movie stand a little better on its own.
We know that the next film is set in the UK and Paris, so I guess we know roughly where that boat was headed. But we have no clue if Credence managed to get cured, whether he’s acting on his own, or if he’s headed to work on behalf Grindelwald. But, no matter what we actually saw in the movie, we can be pretty sure he’s alive.