However, this new issue doesn't have anything to do with the casting. It's got to do with continuity issues.
Just recently, it was revealed by Warner Bros that Professor McGonnagal would be making an appearance in the movie, played by actress Fiona Glascott.
According to Pottermore, McGonagall wasn't born at the time that the movie is set, in 1927.
Fans actually note that she wasn't born in October 1935, which is eight years after she appears as a young witch (in her late 20s or early 30s) in The Crimes of Grindelwald.
Fantastic Beasts: The Crimes of Grindelwald hits theatres November 16.