He likely didn’t think Newt was any threat.
It’s likely that Grindelwald hadn’t considered Newt any sort of threat to him, and didn’t think Newt ‘worth’ killing off. Grindelwald-as-Graves was easily able to fight off several Aurors all at once.
“Graves strides confidently back along the platform, firing spells at both groups of Aurors facing him. Spells fly back at him from all angles, but Graves parries them all. Several Aurors are sent flying—Graves appears to be winning . . .”
- Fantastic Beasts and Where to Find Them (The Original Screenplay)
He’d seen Newt before then and had read Newt’s file - he likely wouldn’t consider a Magizoologist someone who could defeat him in a fight.
“Graves examines the file on his desk.
You were thrown out of Hogwarts for endangering human life—
That was an accident!”
Newt noticed that Grindelwald doesn’t understand things he considers simple, which likely included Newt himself.
How in the name of Merlin did you manage to get . . . ?
The Niffler pokes its head out of NEWT’S jacket, sad to see the pendant go.
Grindelwald doesn’t seem to understand the nature of things he considers simple.
- Fantastic Beasts: The Crimes of Grindelwald (The Original Screenplay)
Newt’s Niffler was able to steal the blood vial from Grindelwald by avoiding notice, and it’s likely Grindelwald similarly considered Newt simple and disregarded him somewhat.