Anti-Climax Boss: Prometheus, who had grown into one of the most brutal, intelligent, monstrous villains that the Justice League has ever faced ends up defeated by a single arrow shot in his head, through his helmet.
Green Arrow single-handedly tracking Prometheus down to his interdimensional lair and instantly killing him with a single wooden arrow when Prometheus had been able to shrug off much more powerful attacks throughout the series.
Critical Dissonance: Despite all of the backlash, the series still received Eisner Award nominations, including one for Best Writing.
Don't Shoot the Message: Working to actively prevent crime and super villains isn't a bad idea in itself. It's the way the heroes go about it that undermines their point.
Memetic Mutation: An unfortunate font choice made the title look more like "Gay for Justice" at a passing glance. Naturally, this caught on fast.
As noted on the trivia page, while he did a fairly lackluster job overall, Lian Harper's death was not James Robinson's fault, although it's one of the first things people usually blame him for.
A fair number of fans, and even people who aren't comic book readers, have conceded that Robinson's statement at San Diego Comic Con 2010 that he was inspired to cut off Roy Harper's arm as a tribute to Iraq War veterans by creating a superhero with a prosthetic that's not cybernetic was in very bad taste, regardless of whether or not it was honesty, a bold-faced lie, or something his editors told him to say. He contradicted this statement in the introduction of Cry's trade paperback, claiming that the editors told him that they wanted to put Roy in this direction. He also made absolutely no mention of his explanation at Comic Con.
The sheer number of times the word "justice" is used, especially "Together, we can be justice."
Prometheus' fight scenes. The man is turned into such a ridiculous Villain Sue that watching him mow down the Justice League is laughable rather than impressive because it's just so damn unlikely.
Take That, Scrappy!: One of the only decent things most readers could agree on was Robinson killing off Endless Winter, a villain from JSA Classified responsible for mutilating and murdering several characters to get their empowered organs, including the original Icemaiden, whom she had skinned alive. Queer readers especially hated her for treating one of DC's few openly bisexual characters so horribly.