In Til Death Do Us Part Batman immediately chases the Joker rather than saving Harley from the "acid", which seems awfully out of character for him considering he very typically invokes Save the Villain... But considering he's also incredibly smart and knows basically every acid type quite well, he probably knew neither of them was in any actual danger and that the "acid" was fake, meaning Harley would be okay and he could focus on the Joker instead.
As a joke in High Bar, Harley is chained up in a chair hora-style after screwing up Joshua's faux-robbery; the mitzvah for a Jewish girl is called a bat mitzvah.
In So, You Need A Crew, there's another reason why Ivy couldn't assist Harley with stealing the warhead from the train: her powers only work when she's in the presence of any flora in the vicinity and given that Harley was trying to steal the warhead from a fast-moving train in freezing-cold weather, there isn't much Ivy could've done even if she wanted to help.
Why does the Joker constantly belittle Bane (with other villains following his lead)? Because, unlike the Joker, Bane is more than capable of taking Batman down by himself. The Joker is frequently demonstrated as being a vain, Alpha Bitch in all but name, so of course he wouldn't like anyone who could potentially usurp his spot as Batman's primary nemesis.
When executing their revenge plot against Maxie Zeus, Clayface disguises himself as Maxie's illegitimate son. As his name and... well, everything about him implies, Maxie Zeus legitimately believes he is the Greek god that shares his name. Zeus (the Greek one) was well-known for siring a great many children in the myths, so it's little wonder Maxie would follow that example and thus leave himself open to being fooled by such a deception.
As seen in L.O.D.R.S.V.P. the Legion of Doom's headquarter has a glass ceiling.
Why does Kite Man act like wearing a kite is such a great power? He convinced himself of this to maintain self-esteem to cope with his parents treating him as worthless since he was born with no powers.
Rather than a bouquet of roses Kite Man gives Ivy a potted rose plant during a date. Showing for all his goofiness Kite Man does understand Poison Ivy more than one might think and how hard he tries in their relationship.
When the gang sees Sy Borgman's mutated sister, Mirie, Clayface says he can't imagine going through life as a giant, deformed thing. This isn't Hypocritical Humor like Dr. Psycho lampshades, Clayface can look completely normal whenever he feels like it and he can speak human language, unlike Sy's sister. Clayface really does have it better than her in so many ways so his pity is well-founded.
A third reason: one of Darkseid's most powerful assets is the Female Furies, a team of elite warriors who (as their name implies) are all women. While Darkseid probably doesn't care if his minions like him, he seems at least pragamatic enough to understand that insulting them unnecessarily might strain their loyalties.
A lot of fans have complained about Nora Fries getting with Maximilian Zeus after the death of her husband. As sad and unfair as it is, it was probably inevitable: the loss of a loved one can lead people to go seek another partner for consolation, whether they are deserving/fitting or otherwise. It was just her bad luck to fall for Zeus.
In "The Final Joke" when Ivy is killed and restored back to life and in the prequel episode "All the Best Inmates Have Daddy Issues", she has thick black streaks running down her face from her eyes, apparently because Ivy sheds black tears. But when Kite-Man breaks off their wedding in "The Runaway Bridesmaid", she sheds normal tears. Ivy sheds black tears when suffering from physical pain (like getting forced into a straitjacket in Arkham, or inflicted with serious injuries), but cries normal tears from emotional pain.
The same black streaks on the Joker's face in the same Arkham episode are from wearing eye makeup. Being vain and a show-off, it's in character for him to wear makeup. And Ivy mentions that he stole her past, he probably stole that look too from her.
Wayne Industries has a bat-shaped tower, a giveaway for any sane person to work out the connection between Bruce Wayne and Batman. But the show's cast is not sane. They're so busy with their own issues and struggles they wouldn't be bothered about this link.
And some could work it out, they just wouldn't give a damn (the Joker is an example of this).
After the Joker, Dr. Psycho is the most deranged and misogynistic character, so it fits that he'd take over as Harley's nemesis in Season 2.
Darkseid of all people giving Harley some counseling over her romantic issues seems odd coming from him, however, given his backstory he could relate: the only person he ever loved was poisoned under orders of his mother, leading to him poisoning her. It's not like he's unfamiliar with a dysfunctional relationship.
While In-Universe it comes as Insane Troll Logic, parts of Dr. Psycho's backstory do have hints as to how he became a misogynist, albeit rather petty reasons. For one thing, he explicitly mentions that it was his mother who encouraged him that he could grow taller and get to go on the Ferris Wheel, meaning that the fact he was never able to put him under the impression that his mother outright lied to him and got his hopes up only to send them crashing down. From another angle, he could have seen it as his mother encouraging him to grow taller so he can go on what was essentially a giant death trap and kill since the Ferris Wheel ended up breaking and killing everyone on it.
In “Dye Hard”, Harley spends most of the episode with Joker who has no memory of his criminal days and has become normal and nice. She does get annoyed with him at times, but she does see how happy he is with his girlfriend and her kids and doesn’t want him to become the Joker again. It could be that since she was his psychiatrist at Arkham, she sees him like a doctor who views a reformed patient and wants the best for him.
In the comics, Catwoman occasionally teams up with Harley and/or Ivy but tends to betray them to Batman for their "own good", so it makes sense that in a show being told from their perspective, Catwoman is instead portrayed as heartless and not caring about their personal struggles for betraying them.
During the vows in "The Runaway Bridesmaid", Kite Man describes an idealized, simple version of the married life he wants with Ivy. While it clearly is used to show that Ivy does not truly want to marry Kite Man, it also shows that he's not ready either. Marriage is not a perfect plan, and the most important part is that neither partner gives themselves up on the other. While he clearly loves her, his dream description about their future essentially says he wants Ivy as his perfect wife, not who she is now, which is a huge red flag in any relationship.
He also states his (very detailed) desired future with her during their wedding vows, rather than consulting her beforehand to make sure she wanted the same things he wanted. (Like having four kids, shuffling them around to things like soccer and ballet, and having Sunday dinner with his Abusive Parents every week.) Again, this shows that he's not mature or far-sighted enough for a serious relationship yet.
Thawed Hearts features a Take That! against the New 52 backstory for Mr. Freeze and gives him his more sympathetic backstory of his wife being frozen so he can cure her disease. Not only is that backstory more popular with fans but there's another reason for using it. It came from Batman: The Animated Series, and what other element of the Batman mythos originated there?
King Shark and Clayface confusing Freeze for Beyoncé and Lady Gaga respectively makes a lot more sense if you consider the timing of the scene: King Shark was reacting to Freeze's dramatic entrance while Clayface was reacting to Freeze's outfit.
Joker expressing surprise to hear Black Manta is black may be why Black Manta never got any (white guilt) awards at the Villy awards. Nobody knew he was black because he was always wearing his suit around other supervillains.
Batman using the bathroom in Catwoman’s place while he kidnapped Frank is more understandable when you remember that Catwoman was his girlfriend at the time and has been to her place several times, making him more comfortable using her bathroom when he’s there.
Joker needing to use a C-Pap machine makes sense considering his famous chemical bath origin (which in this continuity he has gone through no less than three times!) probably did a number on his lungs.
Catwoman pulling a Screw This, I'm Outta Here when she sees Harley's brought her ex Bruce to be tortured for Frank's location not only makes sense because she's dumped him, but she's the only one in the room that knows he's Batman and this won't end well for Harley and Ivy.
The Joker being granted a truly massiveKarma Houdini, despite being the one responsible for unleashing the (presumably nuclear) explosion that caused the earthquake that turned Gotham into "no man's land" in the first place, is possible because there's no evidence or witnesses that Joker did it. Harley, Ivy, and maybe Batman are the only witnesses, and none are reliable or inclined to speak publicly to the press. And proof would need to be gathered by professional experts, but the federal authorities have written off Gotham and are still shunning the place, and local authorities are useless.
Throughout season three, it becomes clear that Harley doesn't want to be a villain anymore and she even wants to help people. This makes sense when you remember that Harley was originally a psychiatrist, someone whose job is to help people. Her need to help others has always been there, it's just been buried beneath all the toxicity that the Joker brought upon her.
Speaking of, if one rewatches the show from Season 1, Harley's redemption arc actually kicked off the moment she left the Joker for good. She just needed a positive relationship and better influences. She has that now with Poison Ivy.
Season Three shapes Batman himself up to be a kind of Big Bad, as he kidnaps Frank as part of a truly crazed plan to use the plant's Resurrective Immortality powers to revive his dead parents. So why is Batman, the very definition of The Stoic, becoming increasingly mentally unstable? Well, in this universe, most of Gotham's supervillains are either dead (the Penguin, Mr. Freeze, the Scarecrow, the Queen of Fables, and Mad Hatter, to name a few), undergoing a Heel–Face Turn (Riddler's running an escape room and dating Clock King, Joker's become a family man, Bane's a bit of a wimp), or part of Harley's Anti-Villain crew (Poison Ivy, Clayface, and Harley herself). As such, Batman no longer has his various nemeses to focus on, and the lack of "big" crimes to solve and thwart is slowly driving him insane. It's long been a running theme that Batman could be considered just as insane as his rogues' gallery, and since that gallery is rapidly diminishing, his own madness is being pushed to the forefront of his mind. It's even lampshaded in "Batman Begins Forever"—Mind!Bruce mentions that he waits for the Bat-Signal to appear every night because he needs to go out on patrol, and now that it's appearing less, he's desperately hunting for something to motivate him at any cost.
Also on that same note it is shown that Batman/Bruce remembers Gotham as a crime Ridden cesspool, while this could be his own biased perspective of that night, it is also possible that Batman/Bruce Wayne refuses to move on from the past and see all the good he has done. Gotham is no longer an absolute shit hole he has made things better but it is never enough for him. He is always driven to do more, he has to do more.
Another thing to note is in the Season 3 finale, Joker arrests Bruce Wayne specifically for tax evasion. A bit of thinking can make one conclude that he specifically has been dodging Joker's universal health care taxes. Joker has mentioned before that "the one percenters are gonna pay for it all", after all. Most likely Bruce has been avoiding his taxes because the more money that gets paid, the more successful healthcare services get and the closer Bruce Wayne as Batman is out of a job.
Poison Ivy being a snarky voice of reason and less of a sadistic, human hating monster in this universe makes sense with the backstory changes they've made. Usually Harley and Ivy meet after Joker's already turned her into his sidekick but here they met while Harley was still a psychologist and had time to actually work on genuinely helping Ivy deal with her issues. By Ivy's own admission Harley made some genuine progress with her before hooking up with Joker and that has allowed Ivy to become a better, more caring and supportive person.
Kite Man's real name is Charles Brown. He's in love with the redheaded Poison Ivy, but she breaks his heart - she's both the Little Red-Haired Girl and the Kite-Eating Tree.
