Credence was upset that Senator Shaw called him a freak.
When Mary Lou Barebone and her adopted children go to tell him about the existence of witches, Senator Shaw calls the Barebones “freaks” and says they all belong in the trash. Credence does seem upset at the time, but it’s clear the insult has really stuck with him when he later meets Graves, and it’s still on his mind. Graves sees he’s upset and asks what it was that someone said to upset him, and in response to that he asks Graves if he thinks he’s a freak.
“CREDENCE stands, head bowed, at the end of a dimly lit alleyway. GRAVES joins him, moving in very close to whisper, conspiratorial:
You’re upset. It’s your mother again. Somebody’s said something – what did they say? Tell me.
Do you think I’m a freak?
No – I think you’re a very special young man or I wouldn’t have asked you to help me, now would I?”
- Fantastic Beasts and Where to Find Them: The Original Screenplay
In addition, Ezra Miller, the actor who plays Credence refers to Credence being called a freak in a way that was deeply affective in the first movie. This has to be referring to Senator Shaw, because he’s the only one in the first movie who called him a freak (a search of the screenplay shows this).
And it’s interesting because we heard in Credence’s narrative in the first film the derogatory term “freak” thrown at him in a way that was deeply affective, right? And I find it really interesting that we find him here in a sideshow, in a freak show, as they were known.
- “Crimes of Grindelwald” Set Visit Interview: Ezra Miller
From this, it’s clear that Senator Shaw calling Credence a freak very much upset him, which then would be why the Obscurus had targeted him specifically - it’s because of that.