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 due with Bruce's old belt and Nightwing's mask. In every version, Dick Grayson was the closest thing Bruce ever had to a son. 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 the fact that 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, who also stole children like Spellbinder in this episode.
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 lead 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 (divorced parents), 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 Peak 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.