The final nail in the coffin for Fantastic Beasts’ political allegory is when Grindelwald namedrops the Holocaust.
Conjuring a vision of the future, he claims that if the muggles continue without magical interference, they’ll start World War II. It’s a twisted version of the “Would you kill baby Hitler?” argument. We don’t know if Grindelwald could prevent WWII, but it creates a scenario where, if the good guys win, they’re potentially fighting for the Holocaust to happen. As well as being wildly offensive, this ties into Rowling’s unpleasant view of muggles.
While Rowling paints a sympathetic picture of muggle-born wizards, the only muggles we know personally are the Dursleys (who are small-minded bullies), Voldemort’s father (the victim of a love potion), Credence’s abusive adoptive mother, and Jacob Kowalski. We never meet a heroic or impressive muggle. Jacob is nice enough, but he’s also an ineffectual buffoon. Combine him with Grindelwald’s assertions about WWII, and these movies suggest that muggles aren’t equal to wizards. They effectively imply that Grindelwald was right all along.