Executive Meddling: According to the Word of God, Batwoman had her civilian identity changed from Kathy Kane to Katrina Moldoff after DC Comics executives voiced concerns about how the negative portrayal on the show might impact sales of the current Batwoman comic book series, which stars the similarly-named "Kate Kane". She was also not referred to by her codename in the episode, except for a throwaway line about a "Bat-lady".
Name's the Same: Shark of the Terrible Trio shares a name with Shark, an actual tiger shark mutated into a humanoid form who had a cameo in "Night of the Huntress!" And neither of them are to be confused with Tiger Shark, of course.
One of Us: Oh so many examples of the fact that the staff is as big of nerds as us, in particular "Mitefall!".
Playing Against Type: Diedrich Bader as Batman. That's right: a guy known for playing The Ditz is the lead. To a lesser extent Will Friedle as the Blue Beetle, who is known for playing characters similar to Bader's.
Screwed by the Network: If giving the final season 13 episodes when the first two had 26 wasn't enough Cartoon Network also managed to anger the fans more by airing the season's episodes with weeks, sometimes a month, between new episodes and without much promotion.
"The Masks of Matches Malone!" episode has not yet aired in the US, after much attention was given online to the innuendo in the Birds of Prey song.
What's more episodes are broadcast with no regularity whatsoever, there can be months between two consecutive new episodes.
What Could Have Been: In "Game Over for Owlman," according to Word of God, it was considered including Terry McGinnis as one of the alternate Batmen. They relented, however, due to it being so early in the series' run - preferring to stand on their own before going so meta.
A fairly minor example, but according to the cover to the comic's first issue Katana was slated to have a wildly different design — one more evocative of mainstream DC Katana, but, like, mostly purple. And pigtails.