The mirror dimension during Albus and Aurelius' duel was never properly explained and didn't make much sense visually. What spells were they using, how did the delluminator technology function exactly. At one point Albus was using it on Credence to isolate and siphon off/extract his obscurus and then that dark mass went right back inside him. What was going on there?

Lally and Jacob are using a portkey and then appear out of the fireplace of the train with a green light behind them indicating they used the floo network.

Those pies in the suitcase multiplying when we know you can't create food out of nothing in the Wizarding World from the principal exceptions to Gamp's Law of Elemental Transfiguration. Though I'm not sure if you can't create food out of thin air but can multiply existing food...

All of the spells were as always ambiguous because of David Yates' blind direction and apparent hatred of differentiating the colors of the spells, the use each spell and complete absence of the latin incantations. Kama at one point just touches his hand on the ground and knocks out 30 adult Wizards. Next thing we know Yusuf Kama is the descendant and heir to Salazar Slytherin himself... This kind of magic prowess was considered on the level of the likes of Dumbledore and Voldemort..

Everything already discussed from CoG like apparating inside Hogwarts, McGonagall's age, Dumbledore's teaching position etc.

Priori Incantatem being a thing in every Wizards' duel, without the wands sharing the same core thus making them twins! Granted it is iconic and has been done before multiple times especially in the Potter films, but those were adaptations of the novels whereas Fantastic Beasts are supposedly "more" canon. Plus they can make the battles more creative and engaging utilizing other forms of magic!

But most importantly, 2 spells blocking Avada Kedavra? How? If this isn't explained (it was a Dumbledore family thing requiring the combined force of 3 or something) this will break the very sacrifice of Lily's protection! There is no spell that can block Avada Kedavra. The only instance in the books we know of something blocking the deadly curse is Fawkes the phoenix when it absorbs it to protect Dumbledore from Voldemort's killing blow at the battle of the Ministry Atrium.

There are more.