Author's Saving Throw: Considering all accusations of antisemitism towards Walt Disney and the Disney company, this movie could have been this. Sadly, it got Canon Banned and Disney treats it like it never existed, which is why we still get jokes about Disney's (possible) antisemitism.
When Miep tries to cheer up Anne when her birthday turned out to be very disappointing, she leads into a big band musical number with a Disney Acid Sequence going on in the background. The whole thing is loud and bombastic to make Anne happy and flies directly into the face of the fact that at the start of the movie, Anne's father clearly stated that they had to try to be as quiet as possible.
The ghost of Kaiser Vilhelm rising from the dead, only to sing his musical number ("I Used To Be Ze Bad Guy"), before playing with Hitler's moustache and returning to the dead.
Rumors have suggested the above scene was contextualised in a Cut Song where Hitler compared his current reign to what it might have been like if the Kaiser had still been in charge (the general gist being that Hitler was a preferable alternative). It was apparently storyboarded but cut for time (not the Unfortunate Implications)
The writers somehow manage to squeeze in a Bar Mitzvah at one point.
It being held for Joseph Goebbels just makes it all the stranger.
The "Dance of the Grateful Flesh" song by Joseph Mengele. Has no real purpose in the story.
Lili Marleen, a classic German love song. It's briefly sung by a lady on the radio and can be heard as a subtle background music during a montage. The soundtrack used during Peter and Anne's tender moments have borrowed a few melodies from this as well.
Ensemble Darkhorse Private Ludwig. He's a well rounded, comedic sidekick, who is also very sympathetic and even helps kill the Big Bad! Even detractors of the movie admit that he was one of the very few things that was positive in the movie.
The Rabbi who Falco punched a Nazi so hard, he smashed into a different country. He's been called 'The Falcon Rabbi'.
Fair for Its Day: Okay, not about the Nazi and Holocaust stuff, but keep in mind: along with The Little Mermaid (released a few months later), this was the first Disney movie to have a well-developed female lead—and in this case, one who actually saved her Love Interest instead of the other way around!
Foe Yay/ Les Yay: Anne and Sgt. Olga have so much of it that some viewers started to wonder if Olga's really a Nazi.
Oh, remember the lady up there who made the Japanese theme song for this? She released a Concept Album of sorts in 1997. Too Soon, perhaps? It's been 8 years so, maybe not. Though you get the uncanny feeling she somehow picked up some inspiration from this after simply writing the song for it. It doesn't help that the album's story is about a girl in Germany in World War II. She had the dream of running away with her lover, but he was drafted, and she couldn’t go to war with him since she was a woman. It's like some sort of alternate ending to the movie and on its own, hearkens to the original intention of the film having a much bleaker ending. Case in point, Anne dying* The album doesn't bring up Anne Frank though but talks about the eponymous "Lili Marleen (spelled Lillie Marlene, in this case)" instead. Spooky.
Love It or Hate It: While it has a vocal, if minor cult following, including some of the staff (who, when questioned, replied "Hey, if you can't laugh at yourself..." and asked to remain anonymous), ask the rest of them and they act like they had post-war depression. The Nostalgia Chick was rumored to, after completing her review of the film, tape Elisa upside down under the door way for four weeks straight without care, and then take the video down in humiliation.
Misaimed Fandom: Although it depicts Nazis as the villains, this movie is disturbingly popular among neo-nazis and white supremacists (largely because of how it treats Mengele). This is probably a large part of the reason for which it will never see home video release.
Nightmare Fuel: Really, when you make a movie about the Holocaust, can you really avoid it?
One-Scene Wonder: On the trainride to Auschwitz, a surprisingly non-zombie guard begins to feel sorry for Anne because her diary was taken from her by Olga, he begins telling lousy jokes which eventually leads to the number "I'm On A Fast Train To Camp Blues". He never appears after this scene. His voice actor wanted to be left uncredited, but his Executive Meddling lead to his name getting top billing, before the title which angered him so much that he refused to work for Disney for years until being asked to dub some roles for Castle in the Sky and the Kingdom Hearts series. That V.A.'s name was Mark Hamill.
She Really Can Act: Wow, Madonna. There was seriously talk about her getting an Oscar, but the movie overall was so hated that she didn't even get nominated.
Star-Derailing Role: For Molly Ringwald. This came after the disastrous failures of The Pick-Up Artist, For Keeps, and Fresh Horses. Rumor has it that Molly received death threats from former fans.
The ending song is often considered the only truly good thing about this movie, and became a pop hit, although officially has no connection with this movie after the soundtrack album plans were scrapped.
The Problem with Licensed Games: The Nintendo Entertainment System game is seen as one of the worst licensed games ever made, and is one of the worst games ever made by Nintendo - indeed, Shigeru Miyamoto himself was head of the team that made it, saying that he wanted to personally "show the world my thoughts on that period in time". Seanbaby, in particular, said "after playing through the game, I can without qualification say that actually going through The Holocaust would be preferable".
That there were plans to make this into an off-Broadway stage musical. (Popularized by Nash Bozard, who thought it was true)
That Disney took everything to do the film and threw it into a fire. (A joke spread by history buffs in reference to Nazi Book Burning. They actually just abandoned most of the pre-production materials in soon-to-be-condemned salt mines)
That Disney are responsible for the film's leak. (Source unknown, this has been neither confirmed nor denied)
Some people have claimed that watching the movie while listening to the Leonard Cohen album The Future results in surprising (and creepy) sync-ups between the music and what's on the screen. If this is the case then it is purely unintentional.
What Do You Mean, It's Not Symbolic?: One of the very last scenes shows Mr. Goebbels, Mouschi and Miep all sleeping together in a pile, symbolizing(?) that people of very different backgrounds can live in peace.
Christopher Lee as the voice of Adolf Hitler. Admittedly, it's just one scene where we never see his face or hear his name, but Olga does address him as "Führer" (and he's actually named such in the closing credits), so it's presumably him.