Graves wondered why it took so long for his colleagues to notice the cuckoo in the nest. By then it has already tipped all the eggs out and well on its way to being a fat parasite. Maybe that was why Newt was able to spot the imposter for what he is. Magical creatures expert indeed.
I should never paint at 2am at this point I am operating on my insanity alone. And I may have been reading too much angstyGraves post-Grindelwald fics of why no one in the MACCU noticed the substitution but a stranger whom he has never met before did (although I’m a fan of Theseus and Graves tots being pen pals and fellow Auror brothers in arms).