I think Graves said something along the lines of "for the greater good" which is the punchline and motto of you-know-who-2. The whole speech he gave was reeking of you-know-who-2's ideology

Also he attacked the ministry with quite expertise.. which ministry employee would do that  ?

The way he interacted with Credence and how he egged on Credence to unleash his power.

I'm sure with prior knowledge of the sort of person you-know-who-2 is.. it ticked off some alarm Inot newts head

Or he could just be absolutely lucky.

I think Graves said something along the lines of "for the greater good" which is the punchline and motto of you-know-who-2. The whole speech he gave was reeking of you-know-who-2's ideology

Also he attacked the ministry with quite expertise.. which ministry employee would do that?

The way he interacted with Credence and how he egged on Credence to unleash his power.

I'm sure with prior knowledge of the sort of person you-know-who-2 is.. it ticked off some alarm in Newt's head

Or he could just be absolutely lucky.