The Mystery of McGonagall's Age
The casting of Fiona Glascott as the young Professor McGonagall in Fantastic Beasts: The Crimes of Grindelwald took Harry Potter fans by surprise. In Harry Potter and the Order of the Phoenix - set in the 1990s - McGonagall said she'd only worked at Hogwarts for "39 years." Over on the Pottermore website, J.K. Rowling had revealed that McGonagall started working at Hogwarts just two years after graduating. Putting all these details together, Minerva McGonagall should have been born in 1935 - and certainly shouldn't have been teaching the young Newt and Leta over two decades before she was born. There's no real fix for this, other than to accept that Rowling appears to have changed her mind about McGonagall's backstory. It's as yet uncertain whether or not this was purely for fan-service, or because the backstory Rowling has fashioned for McGonagall has interesting thematic parallels to Queenie's story in the Fantastic Beasts movies. Perhaps McGonagall will be more important than audiences think.
For all this is frustrating, though, it's not exactly a significant plot hole. Indeed, it's only a problem in light of the broader Harry Potter canon Rowling has revealed on Pottermore; after all, there's no reason a teacher has to stay at Hogwarts all their lives. It's possible McGonagall left Hogwarts sometime after 1945, only to return 39 years before Harry Potter and his friends would attend. This is annoying to committed Harry Potter fans, but it's not really too important.
The Blood Pact
The Blood Pact between Albus Dumbledore and Gellert Grindelwald is a fascinating new twist in the Fantastic Beasts saga, but it does cause some problems. It was presumably forged when Dumbledore and Grindelwald were close friends - closer than brothers, in Dumbledore's words - and when they imagined they would always be side-by-side. As Harry Potter fans know, those expectations were dashed; Albus' brother, Aberforth, saw through Grindelwald, and confronted the two wizards. Wands were drawn, and a ferocious three-way duel broke out at Godric's Hollow, one that tragically led to the Ariana Dumbledore's untimely death. In Harry Potter and the Deathly Hallows, Albus reflected that he didn't know who was responsible for the spell that killed Ariana; he believed all three wizards were casting Killing Curses.
But the Blood Pact apparently restrains Dumbledore and Grindelwald from acting against one another, so how could that three-way duel even happen? It's important to remember, though, that the Blood Pact is a brand new idea in Harry Potter canon; at present, we have simply no way of knowing how it works. Does it actually stop the two wizards from fighting each other? Or does it mean that, should Albus kill or injure Grindelwald, he will suffer the same fate? The latter is suggested by the fact their blood is mixed within the Blood Troth, suggesting they would suffer and die together. If this is, indeed, the case, then it gives a sense of how desperate and dangerous that three-way duel was. Both Albus and Grindelwald were risking their own lives when they turned their Killing Curses upon each other. It will be interesting to see if Rowling takes to Pottermore to clarify the issue, and explain how the Blood Pact really works.
Credence Barebone is Aurelius Dumbledore
The end of Fantastic Beasts: The Crimes of Grindelwald reveals the shocking truth of Credence's real identity as Aurelius Dumbledore. This revelation has shaken the Harry Potter fandom to its core, as it seems to contradict everything we already knew about the Dumbledore family. After all, by the 1890s, Dumbledore's father had been committed to Azkaban for life imprisonment, and his mother died in 1899. Credence would seem to be far too young to be a Dumbledore. And yet, while Grindelwald is hardly a trustworthy source, the script clearly intends audiences to believe this is true. That's why Fantastic Beasts 2 sees Albus disclose a Dumbledore family legend about Phoenixes, only for Credence's pet bird to turn into a Phoenix. Even Credence's first name Aurelius is intended to signpost this; "Albus" means "white," "Ariana" refers to "silver," and "Aurelius" is "golden." The name Grindelwald gives to Credence fits perfectly with the naming traditions of the Dumbledore family (Aberforth excluded).
On the face of it, there are two possibilities. The first is that Albus' mother Kendra was seeing another wizard before her death, and even gave birth to a child; perhaps the relationship would have been scandalous, and so the infant was sent over to America. That's possible, but the timeline doesn't really fit - Credence is too young. The other possibility is that Albus' father Percival slept with another inmate at Azkaban, and left her pregnant. That seems more likely, as the exact date of Percival's death in Azkaban is unknown; again, there'd be just the right note of family scandal to explain why the infant was taken over the Atlantic. The credits claim that the woman with the young Credence was his aunt, which probably means she was Albus' spinster aunt Honoria, acting to preserve what remained of the family reputation. It's unknown if Albus is aware he has another brother; apparently Rowling has told Jude Law, but he's understandably keeping quiet.
But this isn't a plot hole. Rather, it's a major plot point that has yet to be resolved, and will clearly be important in Fantastic Beasts 3. Ezra Miller has reassured fans that they need to trust J.K. Rowling. And he believes that Fantastic Beasts 3 will revolve around the theme of "why" is Credence - why is he a Dumbledore, why was he sent away, why do the history books not record his existence in the Dumbledore family line? If this is the case, audiences need to accept that this isn't a plot hole; it's a story that has yet to be told.
Rowling is a skilled storyteller, and, as such, Harry Potter fans would be wise to be patient. It's entirely possible that there's a reason Rowling has broken her canon, and that the Fantastic Beasts story will end in such a way as to neatly resolve every issue her prequel films have raised. Only time will tell.