The biggest plot holes in the Fantastic Beasts movies
Despite being a spinoff of the Harry Potter franchise, Fantastic Beasts pokes a few holes in the overall plot and canon.

The "Fantastic Beasts" films failed to achieve the same level of recognition as the "Harry Potter" series, with "Dumbledore's Secret" being the lowest-grossing film to date. This has led many to question whether the franchise will continue as it could blow up making high movie budgets too risky.
It's hard to say exactly why Newt's wizarding world story didn't draw audiences to theater. Since the author J.K., some have speculated that politics had something to do with it. Rowling herself has made disturbing headlines on several occasions, and the recasting of the infamous Johnny Depp as Gellert Grindelwald has many fans enthusiastically boycotting it. Even without addressing these real-world issues, however, Fantastic Beasts disappoints Harry Potter fans by punching holes in the wizarding world canon. From the intricate wand lore to the involvement of characters like Minerva McGonagall in the 1930s, Fantastic Beasts contains many plot holes that cannot be ignored.
Gellert Grindelwald Should Have Lost The Elder Wand's Allegiance

Grindelwald and Voldemort are unique villains in Harry Potter, but the Elder Wand is what they have in common. Since the death stick was revealed, the death stick has become an important item in Harry's story It can change allegiances in difficult situations, helping the Boy Who Lived achieve ultimate victory.
However, this crucial detail about the wand was immediately dropped when Tina Goldstein disarmed Grindelwald at the end of the first film. The wand she confiscated might not be the Elder Wand, but Harry Potter reveals it doesn't have to be. Therefore, according to the setting, Tina should be its master now, and it should no longer perform well against Grindelwald.
Minerva McGonagall Shouldn't Be A Hogwarts Teacher Yet

It was exciting to see a young Professor Minerva McGonagall in The Crimes of Grindelwald and Dumbledore's Secret. Actress Fiona Glascott brilliantly replicates Maggie Smith's performance as the stern professor. However, according to McGonagall herself in Order of the Phoenix, she wasn't supposed to be teaching during Newt's adventures.
In an evaluation by Dolores Umbridge (1995), Professor McGonagall stated that she had taught for 39 years. That means she's from the 1950's. Fantastic Beasts takes place in the 1930s, when McGonagall was probably not a student.
There Is No Apparating Into Hogwarts— No Exceptions

The Harry Potter films have broken some of the most important titles Rules of Hogwarts Castle. Die-hard fans know that on the grounds of Hogwarts, Apparition is completely out of the question, even for Dumbledore. Still, the movie has the headmaster declare that the rule doesn't apply to him.
While changing the rules for someone like Dumbledore is somewhat acceptable, Fantastic Beasts has seen several other characters appear at the foot of the castle. It seems like a small detail, but when so many conspiracies about the safety of Hogwarts depend on it, ignoring it becomes a major hole.
Where Is The Deathly Hallows Symbol?

In Harry Potter and the Deathly Hallows, Victor Krum becomes angry when he notices the Deathly Hallows symbol on Xenophilius Lovegood's necklace. He calls out Grindelwald's mark, telling Harry that it is a sign of the Dark Wizard's actions. In Krum's country, it has become the equivalent of the swastika.
Harry Potter fans know the true meaning of the Deathly Hallows, but it's odd that it hasn't been featured in the Fantastic Beasts series so far. Grindelwald built a loyal following and made massive power moves. The "he" logo should be everywhere, but it is completely absent.
The Blood Pact Doesn't Fit With Dumbledore and Grindelwald's Story

Dumbledore reveals to Harry in Deathly Hallows that he is too scared Confront Grindelwald for their complicated history. However, after it became clear he had no other choice, he confronted his old friend. Of course, Fantastic Beasts reveals a more complicated story. Dumbledore's desire to keep some details private is believable, but there are still inconsistencies between the two versions.
In various accounts, Ariana Dumbledore was killed in a duel between Albus, Aberforth, and Grindelwald. However, according to Where are the Fantastic Beasts, the young couple had formed a blood bond long ago. Since this ensures that neither of them can take action against the other, a duel is impossible and Ariana doesn't die - it's just not appropriate.
Avada Kedavra Has Been Heavily Downplayed

Voldemort's signature spell in Harry Potter is the "Avada Kedavra" or Killing Curse. An important detail about this spell is that it cannot be blocked, and Harry is the only one who survives it. However, in Fantastic Beasts and Where to Find Them, powerful spells are greatly downplayed.
The audience sees the transcendental spell again (which was supposed to be a one-time event between Harry and Voldemort's wand) in Fantastic Beasts and Where to Find It as a way to stop the Killing Curse. Then in Dumbledore's Secret, the mother Qilin needs to use spells to attack a few times before slowly dying. To make matters worse, Albus and Aberforth later stopped the curse in order to save Credence - which made Harry's survival even more unremarkable.
Grindelwald Removing Yusuf Kama's Memories Shouldn't Have Been So Easy

Several questions about Yusuf Karma remain unanswered at the end of Dumbledore's Secret. His allegiance is unknown for most of the film, and when Grindelwald erases his memory of Leta Lestrange, nothing seems to keep him fighting for Dumbledore. Still, he eventually pulls through and protects Theseus.
Did Yusuf keep his memory? If not, why didn't he actually join Grindelwald? The whole subplot seems to serve no purpose other than to keep the audience guessing without providing answers. What's even more frustrating is that memories are never permanently erased in this way in Harry Potter, so the situation is even more confusing.
Dumbledore Never Knew About The Room Of Requirement

In Harry Potter, the Room of Requirement is a key location for several subplots. Because Voldemort hid Ravenclaw's diadem there, it was especially important in the hunt for the Horcruxes. In Dumbledore's Secret, audiences are happy to see a familiar room again, but Dumbledore's understanding of it differs from Harry's story.
Throughout most of Deathly Hallows, Hermione refuses to search Hogwarts because she believes that if there is a Horcrux there, Dumbledore will find it. However, Harry later realizes that Dumbledore never found the Room of Requirement, as he has mentioned believing it to be the disappearing bathroom in the Goblet of Fire. That's how Harry finally discovers where the diadem is - the only place Dumbledore won't be looking. It's possible that Harry was wrong in his reasoning and was still lucky enough to find the Horcrux, but if that were the case, the excitement of Harry's discovery would be much lessened.
The Qilin Wouldn't Have Picked Albus Dumbledore

The hardest lesson Harry learns in Deathly Hallows is that his hero, Albus Dumbledore, is far from perfect. Even after he gave up his goal of ruling Muggles, he did several unimaginable things for the greater good. He raised Harry knowing he would be sacrificed, and allowed the student to put himself in danger to tempt the forces of fate.
Therefore, it is meaningless for Kirin to think that Dumbledore is "pure in heart". He's certainly not evil, it takes someone willing to manipulate the environment (even to other people's damage) to a better outcome for all. Still, his actions certainly disqualify him as the first choice of goodness.