Terry and his little brother's black hair? Despite neither of their parents having black hair, Terry's father's reproductive data was overwritten by Bruce's in the hopes of creating a new Batman.
We already know that Terry and Bruce aren't at all enthusiastic about Max joining in on their crime-fighting, even after she gets in on Terry's secret identity. We know Terry's reason—he simply doesn't want her to get hurt—but Bruce's reason only makes a whole lot more sense after watching Return of the Jokerand seeing, in flashback, what the Joker did to Tim. Simply put, Bruce doesn't want any more sidekicks getting the same kind of treatment; and it's also what led to his past sidekicks leaving him.
"Lost Soul". When the Batsuit is taken over by an evil AI, Terry makes do with Bruce's old belt and Nightwing's mask. In every version, Dick Grayson was the closest thing Bruce ever had to a son, other than Damien Wayne. Then, in JLU, what do we find out Terry is?
Bruce's loyal guard dog is named "Ace". In JLU Bruce stayed with Ace until she died. Now "Ace" is serving as the only companion that the former Dark Knight has during his darkest hour.
May be an unintentional example but the Terrific Trio's name. At first, it just appears to be an Alliterative Name based on the Fantastic Four but then take note of how in the past, the word "terrific" used to have a much different connotation, one signifying something bad or horrible the same way that the words "terror" and "terrifying" continue to do. In this sense, the name "Terrific Trio" has a harsher and more disturbing Double Meaning given their eventual tragic breakdown and demise.
In "Hooked Up", when Donnie is first taken out of his VR simulator by Spellbinder, he's told "It's time to pay the piper," not just referring to the saying "He who pays the piper calls the tune," but to The Pied Piper of Hamelin, who also stole children like Spellbinder did in this episode.
In "Once Burned", King and Queen of the Royal Flush Gang are held hostage by the Jokerz and Melanie/Ten has to rob a gangsters' poker tournament as part of their ransom. But when you think about it, that ransom seems too specific and unlike how the Jokerz operate. It makes much more sense when it's revealed that the whole thing was a loyalty test by King and Queen. Their task is not only hard, but it fits with the RFG's M.O.: The targets fit into the card theme (as it's a card game being robbed), and the RFG is demonstrating their superiority over "commoner" criminals by treating them as pawns and targets.
In "Shriek" Powers turns down legitimate use of Shreeve's tech saying that dynamite's cheaper. Even if it is cheaper, dynamite requires a full crew to plan and place and other equipment such as detonators, wiring, and a plunger to set it off. There could be other costs or a longer schedule depending on the project, such as safety harnesses. Not to mention that Shreeve takes down the old GCPD in minutes, while fighting Batman. The suit is cheaper, Powers just tricked Shreeve because the latter was naive and because Powers was ticked that Shreeve scared him with his opening demonstration.
In "Heroes" the Terrific Trio, a group of accidentally created heroes, learn they were a product of an experiment and begin causing destruction. When Batman tried to appeal to the leader Magma's heroic side, he retorted that he was no hero but merely an accident, because he was never given a choice to be a hero. Later, in "Epilogue" when Terry learns he is Bruce's genetic match, he himself comes to feel his choices were taken away from him.
In "Terry's Friend Dates a Robot", we see Cynthia, a Ridiculously Human Robot built and programmed to be Howard's girlfriend. Throughout the course of the episode, she proves to be Nigh-Invulnerable, Super Strong, and fast enough on the reflexes to catch one of Terry's batarangs, despite ostensibly being created as a G-rated sex bot. Well, the factory Howard bought Cynthia from also builds synthoids for combat, and Bruce Wayne orders synthoid replicas of people he knew in his heyday as Batman to use in Terry's combat training. Which, knowing Bruce, would include other members of the Justice League, in case circumstances ever forced Terry to go up against them in combat. Cynthia's abilities and temperament match those of Wonder Woman, suggesting that the dealer may be using the templates reserved for Bruce Wayne to make his illegal synthoids.
In "Sneak Peek" Ian Peek began to feel the effects of the invention he used to find out Terry and Bruce's identity, unable to control it, his body begins to lose control of itself and slowly begins to phase through the ground itself. The only thing stopping him is death as he will forever being moving back in forth in the Earth's core. One interpretation can lead one to think that the only thing dragging Peek to his fate was the weight of the sins. It's what Bruce said in the end that can describe the ending of a egocentric man like Ian,
Assuming that Bruce learned about Terry's genetic relation to him way before the two actually meet, much of his actions does makes sense.
His appearance to confront Terry's pursuers? He's already been watching over his son and heads out to help him.
His complete omission of Andrea Beaumont from his photos of his love lives is probably due to the fact that she took part in the near murder of Warren and Mary, the same way his parents went through.
Superman's knowledge of Terry's true lineage is due to Bruce telling him about it.
In "The Last Resort" we see a little hint at the improved relationship between Terry and Mary. Parents are sending their kids to the titular resort by the droves, many, it's implied, for rather minor offences. Now Terry actually used to be a troubled kid, he went to Juvie for three months before he became Batman and in the first season episode "Slappers" Mary was willing to believe the worst when she found a titular Slapper in Terry's bag, suggesting a low level of trust between the two of them. However Terry is one of the few students not to be sent to the Resort. Clearly this shows that in the intervening time their relationship has improved quite significantly to the point that she now trusts him enough to believe he didn't need to go to the resort.
We know that Terry's parents broke up prior to the start of the series, but it's possible that the fact that neither Terry nor his brother resemble EITHER of his parents could have led to suspicions of cheating on Mary's part, which itself could have been a major factor leading to the divorce. And anyone who's seen Epilogue knows that neither parent was at all unfaithful. It was just that since the McGinnises were similar to Bruce's parents, they were chosen to have his reproductive data overwritten by Bruce's in an attempt to create a new Batman. In other words, simple bad luck could have caused this divorce.
Amanda Waller planned to have Terry's parents assassinated when Terry was just 8 years old, hoping that Terry would become new Batman. However, who's to say that killing Terry's parents would have same effect on Terry as it did on Bruce? The whole thing might have turned out the other way and Terry might have possibly turned out to be incredibly malicious supervillain, instead of the new hero Amanda Waller wanted. At the first sign of trouble in Terry's happy family life (his parents' divorce), what does he do? He runs with a bad crowd, ultimately ending in a three month stint in juvie. What would have happened if his parents had died? At best he would have become an anti-hero on the level of Jason Todd. At worst...
The device Ian Peek used made him intangible by vibrating his molecules. Meaning what happened to him is exactly what would happen to The Flash if he ever lost control of his powers.
Inque's daughter Deanna never makes an appearance again after "Inqueling". Inque does. And it's a safe bet she wasn't exactly pleased that her daughter tried to kill her. Do the math and you'll probably figure out why we never saw Deanna again...
Remember when Ra's Al Ghul revealed that he uploaded his brain into Talia's body? We only get his word that she complied, but who's to say Talia wasn't completely on board with the idea?
From "The Winning Edge", Bane's caretaker is the only person left to make Venom after Bane went into a vegetative state - with his own brain-dead state, Bane probably doesn't have much time left to live.
That scene carries a lot of implications about what Venom does to a body that's not already modified and conditioned to handle it. With a little Fridge from the rest of the DCAU, a Venom overdose may rank alongside being gassed with Joker Venom as one of the most horrific ways a person can die in the DC Universe.
The Venom overdose causes Chapell to scream in pain as his body bulks up uncontrollably, leaves him in so much pain that it temporarily forces him to his knees, and leaves him barely coherent when he resumes the fight. Compare this to Bane's inaugural fight with Bruce, when a broken Venom pump reduced Bane to a barely-coherent screaming wreck as he came closer to death from overdose. The fact that the DCAU never clarifies what is causing that amount of pain during a Venom overdose leaves one to wonder if a person's muscles are trying to tear themselves off his bones or trying to snap his bones in half with that much Venom in his system.
Any time Bane juiced himself up for a fight, the Growing Muscles Sequence often comes with an accelerating Heartbeat Soundtrack, leaving the implication that the drug is overclocking his heart rate and respiration to compensate for the increase in mass. At the kinds of doses Bane took in for his fights with Bruce, a person whose body isn't accustomed to receiving Venom would be asphyxiating and having a stroke at the same time. So you basically suffer brain death while your body feels like it's ripping itself apart.
When Max regains consciousness in "Curse of the Kobra Part II" and seems surprised by her new outfit, her "servants" explain it's because "when you arrived here, your clothes were torn." We saw her unconscious in Zander's car after the scuffle in her apartment, and her clothes weren't torn then, so... how did they get torn between then and now? What did Zander do to her in that time...?
"Rebirth Part I" presumably has Warren killed in a brutal fashion. Terry beats himself up afterwards for not being there and helping his father (having no idea that the Jokerz weren't responsible)... but the fight he later has with Mr. Fixx indicates that if Terry had obeyed his father and stayed home, he would've been killed too.
"April Moon" As soon as Terry utter the words "April Moon" (The fail safe), all the thugs that The Doctor operated on began to have their mechanical parts fall of, especially one poor thug who had his legs and arms modified for said mechanical parts, only to see them all fall apart. It is especially frightening to hear them yell in pain, it's not like a prosthetic arm or leg, no they're feeling that pain.
The ending was as twisted as possible. Terry relayed the events to Bruce, mentioning that The Doctor was with him and he knows about Bullwhip's scheme about his wife cheating with him. Bruce asked Terry if Bullwhip saw The Doctor with him, Terry doubts it as he hid him before anyone saw him. Bullwhip only saw Batman that night, not with the Doctor. The final scene has Bullwhip casually mentioning that April is fine and he'll be done after one more surgery, telling the Doctor to go all out with him before the Anesthesia kicks in. The Doctor seems happy to oblige as the drill closes in and the scene fades to black.
Bullwhip: Don't hold back, Understand? The Doctor: I understand. No holding back.
And remember, April Moon was in on this whole scheme with Bullwhip, cheating on The Doctor, and she doesn't know either. April might very well be the next victim.
In "Lost Soul", the digital copy of Robert Vance was willing to drown Batman and sacrifice his own grandson to accomplish his goal. It makes you wonder what the real Robert Vance was like before he died. Was he as sadistic as his digital copy? They DID mention the copy having the same personality as his human self.
The way Robert Vance "dies" is pretty disturbing. The last thing you hear is a child's voice slowly fading away.
In "Payback" the titular villain , a child named Kenny, is arrested by the police for attempted murder of several individuals. Even if he does reform after getting out of juvenile hall, he'll spend the rest of his life marked for this.
The Batman Beyond comics only make the situation worse. After getting there Kenny was mercilessly bullied and abused by the older kids until he couldn't take it and was Driven to Suicide.