When Newt engages in the fight against Grindelwald's lackeys, it is his right hand that is injured and gets bandaged; however, when Newt and Theseus enter the pub in Hogsmeade, it is Newt's left hand that is bandaged; but when they are speaking to Dumbledore the bandage is back on Newt's right hand.
Jacob exiting the fireplace on the train, after leaving New York via the "portkey", indicates they made a stop somewhere along the way, as portkeys and the Floo Network are not open to each other.
The flames on all kerosene/paraffin lamps in the movie don't flicker as real ones would. This is because they're LED bulbs.
No tie knot can untie itself as shown in the prison.
Newt tells Tina, "You've changed your hair," but it's the same length as in the photo in his suitcase. [This goof makes no sense. Changing her hair does not necessarily mean she got a haircut. It is clear that Tina's hair is more wavy in this scene compared to her straight hair from the previous film. Also, despite this goof saying her hair is the same length, it is actually slightly longer.]
At the end of movie when they are in Queens and it is snowing, nobody is leaving any footprints in the snow showing it is all CGI.
The announcer at the railway station in Berlin says Bratislava even though an announcer at that time and place still would have used the old name Preßburg instead.
On the building across the street from Jacob's bakery, just above the bus stop bench, is a sign that reads "TO LET". This is a British phrasing. In Queens, the sign would read "FOR RENT".
There was no reason why a Qilin (a 1/ wild female with 2/ babies to protect and 3/ vision into the future) would not react to the approaching foes (she should have been warned by scent, noise, or sight).