Accidental Innuendo: The Top's quip about how "Once again, it looks like you're the bottom, and I'm..." well, you get the idea.
Alternative Character Interpretation: Flashpoint Aquaman. Is he really grieving and regretful and he feels guilty about his infidelity with Mera and he wants revenge against the woman who killed his wife? Or avenging Mera is only his duty as Atlantis' ruler and he still is in love with Diana? It's also implied that he deeply blames Mera for the war between Atlantis and Themyscira...
Author's Saving Throw: A controversial element of the comics since Barry Allen's revival was that it was Zoom who originally traveled back through time and murdered Nora Allen, thus setting up Barry's new motivations in the post-Crisis world. Fans thought that it made no sense that Barry going back to fix what Zoom had already changed would lead to the end of the world instead of just removing things like Henry Allen being in jail. The movie only hints at Zoom's involvement, so it instead allows the plot point to be seen more as a selfish act as the plot suggests.
Complete Monster: Eobard Thawne, aka Professor Zoom, is the Reverse-Flash and opposes everything Barry Allen stands for. Thawne hires various other Flash villains to break into the Flash museum. Thawne straps bombs to the villains he hired after they defeat Flash, planning to blow up the Flash museum and several surrounding blocks, just so the Flash will be tormented knowing that several innocent people will die with him. After his initial defeat, Thawne mocks Flash over the fact his mother died. After Flash uses his speed to travel back in time and save his mother, the world is sent to a twisted alternate state, in which a war between Atlantis and the Amazons has caused massive devastation. Thawne delights in Barry's agony at the new world and enjoys the carnage as it makes his nemesis suffer. When Barry tries to fix the realities, Thawne tries to stop him, meaning he is willing to cause and allow the deaths of countless innocents, as well as himself, solely to satisfy his hatred of Barry.
Flashpoint Deathstroke, being as badass as any other version of the character and featuring a Role Reprise from Ron Perlman to boot.
Yo-yo has about 2 minutes of screen time, yet is fondly remembered for being a badass alternate version of Harley Quinn capable of going toe to toe with Flashpoint Batman.
Evil Is Sexy: Flashpoint Wonder Woman. Lampshaded by her when Steve Trevor confesses that he thinks Lois Lane is "one of the most beautiful women he's ever met" to which Wonder Woman replies: "Until now, you mean".
Genius Bonus: When the Amazons wiped out the UK it was stated 32 million were killed. The population of the UK is 64 million. And with the Amazons being who they are heavily suggests they wiped out the male half.
He's Just Hiding!: A few fans have called the deaths of Flashpoint Deathstroke and Clayface as situations they could have survived, even though realistically their prospects don't look good regardless.
Jerkass Woobie: Flashpoint Batman, who's in fact Thomas Wayne. This version of him watched his only child die and then after that his wife turn into a maniac and his world go to hell in a hand-basket. It's hard to fault him for his bitterness following all of this.
Professor Zoom crosses it either when he plans to kill numerous innocent civilians in Central City to spite the Flash, or when he makes it abundantly clear that he's fine with the world ending just because he knows the Flash is suffering because of it.
Flashpoint Wonder Woman was way over the line when she murdered a rightfully angry Mera and sent Aquaman her head and kept her crown as a trophy, but murdering the young Billy Batson destroyed any semblance of sympathy for the character.
Aquaman's overly-buff design is impossible to take seriously, especially compared with the relatively small size of his head. Made even worse by the fact that his Flashpoint self is one of the major antagonists and is supposed to be intimidating.
Superman's design (also overly buff and with an odd, wrinkled face) is also pretty hard to take seriously.
The overly pronounced lips on some of the characters.
During the film's otherwise-gripping climax, the models for both Flash and Thawne inexplicably become rather-obvious CGI.
While C. Thomas Howell does an excellent job voicing Thawne throughout the film, his "Ah-ah-ah" at the film's climax sounds rather stilted in comparison to his Breaking Speech just moments before.
One-Scene Wonder: Martha Wayne's flashback appearance where she grieves young Bruce. It only last for exactly one minute, but everyone remembers it very well for how terrifyinglytragic it is.
Spiritual Adaptation: This is more a Flash movie than a Justice League movie, but it was probably given the title Justice League in an attempt to avoid poor sales suffered by the DCAUOM's Green Lantern and Wonder Woman (i.e. not Batman/Superman/JL) titles. It can also be argued that The Flash: The Flashpoint Paradox would have sounded terrible.
The members of the Resistance (including Lois Lane), who have barely any presence during the final battle, with only Grifter getting a few scenes to himself.
Orm, who is a major villain in the original story, is essentially reduced to a cameo, and gets Killed Offscreen. This despite him being Aquaman's most famous antagonist and a top threat within his forces.
And then there's the team of supers that Cyborg had been recruiting. The Shazam kids are the only ones to actually join the war, to the point it's a mystery why the film even bothered to introduce them in the first place.
Flashpoint Joker. Batman's intro scene has him interrogating Yo-yo about the villain's whereabouts; and the conversation at the Bat-Cave hints that the Joker may be an even greater threat than Wonder Woman and Aquaman. In reality, the Joker arc is Adapted Out, with her single appearance being in a flashback as Barry learns how the new timeline came to be.
Mera confronting Diana about her affair with Arthur. While Diana is sharpening her sword. It doesn't end well for Mera.
Barry's first visit to Wayne Manor after time is changed is made of this. First, he acts like he can walk into the Manor without a call like he normally can, despite being aware he's in an alternate timeline. This results in Batman beating a powerless Barry. When Barry figures out he's talking to Thomas Wayne, not Bruce, he says this out-loud instead of keeping it to himself, then when asked about his knowledge, he forgets that it was a touchy subject for Bruce and probably would be for Thomas as well, and says Bruce's name. Both of these result in Thomas breaking one of Barry's fingers each.
What Do You Mean, It's Not for Kids?: This is one of DC's darkest and most violent films, as the PG-13 is pushed pretty far in regards to the violence and gore. Up in Canada this got the PG rating when it is more than worthy of the 14-A rating. In particular, it's hard to believe that Professor Zoom's death, shot in the head by Batman with a bloody wound so large, you can see through the other side, would garner a PG-13 rating.
Flashpoint Superman, like in the original source, although possibly his life was worse in this adaptation than the Flashpoint comics. Flash and Flashpoint Cyborg seem to have been his first friends in his entire life, and then one of them dies in his arms.
Flash himself becomes this. In addition to his mother's Death by Origin Story, there's also how his attempt to save her creates the Flashpoint world and then he has to willingly sacrifice his mother to set things right in the end. Ouch.
Billy Batson/Captain Thunder. Given the fact that the latter suffered a scar across his face, no doubt at the hands of Wonder Woman, so no doubt Billy has went through some serious shit while still a kid no less. Him being murdered by Diana was the icing on the cake.