Executive Meddling: The Bat-Editors constantly threatened to yank Robin from the book unless the writers obeyed their edicts on how he could be featured; most notably, Robin could not be used in any battle that took place in public, according to the "urban legend" policy in the Bat-books.
This resulted in a couple of Take That jokes during a reality show story ("Did the all-concealing shadows just say ouch?"), including Robin creating the hero identity of "Mr. Sarcastic," a shaved-head Shout-Out to Spider Jerusalem (and possibly to Protector, a Robin expy created for 80's Teen Titans PSA comics when licensing contracts prevented the Boy Wonder's use).
Fake Nationality: Despite the series using voice acting where this trope is less of a problem, this is actually averted more often than not. Hispanics are voiced by Hispanics, Asians are voiced by Asians...although one could argue that the effect is ruined when Lex Luthor has a better Japanese accent than the Japanese character voiced by an ethnically Japanese woman.
Fandom Nod: In the series premiere, you have a citizen asking if Speedy is the Flash's sidekick, and when someone responds that he's Green Arrows, the first guy says "that makes no sense," echoing a fair amount of comic book fans who didn't get Speedy's name (especially those introduced to him in crossovers).
Artemis being the comic book villain Artemis Crock. (Because the only other DC characters named Artemis are a redheaded Amazon and the Greek goddess.)
Six of the seven leaders of the Light being Vandal Savage, Lex Luthor, Ra's al Ghul, Queen Bee, Ocean Master, and the Brain. What no one expected was Klarion being the seventh one.
Cheshire being Artemis's older sister. (Not in the comics.)
Also, Sportsmaster being Artemis's father. (As in the comics.)
Sphere being the Super-Cycle from the Young Justice comics.
M'gann's personality being lifted from a TV series called Hello, Megan!. (Hinted several times.)
M'gann being a White Martian. (As in the comics. Hinted even more than the above.)
Guardian being Red Arrow's uncle. (As in the comics.)
Sort of. He's actually another clone of Roy Harper, programmed to think he's Roy's uncle.
Prince Orm being Ocean Master as revealed in tie-in comic issue #14 (As in the main comics.)
Conner being the half-human hybrid clone of Superman and Lex Luthor. (As in the comics, though a Retcon made after the Young Justice comic series which included him.)
Starro being the tentacle organism found in Atlantis and being involved in the Light's plot. (Even though it wasn't named, nothing else fits.)
Impressively, some predicted that the term Sportsmaster used to describe Red Arrow, "Broken Arrow", in the episode "Targets" would be significant in the future. It was: "Broken Arrow" is a shut-down command implemented into Roy (The Mole) to retrieve information or to program him even further.
The fact that Season 2 would start with a time skip.
And once an image of Nightwing was leaked, some people guessed a more specific number, namely 5.
Aqualad quitting The Team and joining Black Manta, and the reason for which being Tula's death. (Because of leaked images of toy packaging.)
Superboy (Conner Kent) and Miss Martian (M'gann M'orzz) = SuperMartian
Robin I, later Nightwing (Dick Grayson) and Zatanna = Chalant
Cheshire (Jade Nguyen) and Red Arrow (Clone! Roy Harper) = RedCat or Cheshroy
Guardian III (Mal Duncan) and Bumblebee (Karen Beecher) = GuardianBee
Tye Longshadow and Asami "Sam" Koizumi = Team Headbands
Eduardo "Ed" Dorado and Asami "Sam" Koizumi = Vest Duo
Lagoon Boy (La'gaan) and Miss Martian (M'gann M'orzz) = Angelfish
Artemis and Red Arrow (Clone! Roy Harper) = Longshot
Wonder Girl (Cassie Sandsmark) and Arsenal = Wonder Gun
Wonder Girl (Cassie Sandsmark) and Blue Beetle III (Jaime Reyes) = WonderBeetle
Robin, later Nightwing (Dick Grayson) and Artemis = Traught
Blue Beetle III and Impulse (Bart Allen) = SpeedBuggy
Artemis, Miss Martian (M'gann M'orzz), and Aqualad (Kaldur) = Symbiosi
Wonder Girl (Cassie Sandsmark) and Lagoon Boy (La'gaan) = WonderChum
Aqualad (Kaldur) and Red Arrow (Clone Roy Harper) = Koy
Captain Marvel (Billy Batson) and Zatanna = Mazahs
Aqualad (Kaldur) and Artemis = SeaArrow
Superboy (Connor Kent) and Wonder Girl (Cassie Sandsmark) = Powerhouse
Internet Counterattack: 10 hours before it was supposed to air, DC Nation was mysteriously pulled from Cartoon Network's schedule and replaced with HTTYD: Riders of Berk and Johnny Test with no warning at all. Word got out and angry Young Justice and Green Lantern: The Animated Series fans began to rage on various forums and sites alongside one of the guys who worked on Green Lantern (and who had just done a USA Today interview talking about the show) and a newcomer whose very first short, Amethyst: Princess of Gemworld, was supposed to premiere the same day. In attempt to do damage control, Cartoon Network posted that DC Nation would be back in the January of next year... which didn't really improve matters due to the fact that the block had just come out of hiatus TWO WEEKS prior to this. As of October 14th, a petition has been made in an attempt to get the block back sooner and fans have begun to boycott the channel.
Up to Eleven with the announcement that Young Justice and Green Lantern: The Animated Series would not be returning after airing their current seasons. Cartoon Network and DC Comics were forced to issue a (bland, uninformative) statement less than three days in, while #SaveYJandGLTAS was trending on Twitter for about an hour the first Saturday morning.
Lying Creator: Overlapping with Exact Words. Before the second season began airing, Greg Weisman stated that it would continue on minutes after the last season finale ended. While this is technically true, it is very misleading, since the scene that does take place right after the first season lasts less than a minute and is followed by a five year Time Skip.
Name's the Same: Artemis' mother used to be a villain named Huntress. She's unrelated to Huntress of the Batman-related DC books. Her comics counterpart was created first (by some decades) and was renamed "Tigress" once the other was introduced.
Rocket was voiced by Miss Kittie in "Usual Suspects," "Auld Acquaintance," and "Satisfaction," and Denise Boutte in "Intervention."
Flash (Barry Allen) was voiced by George Eads in Season 1 and the Season 2 episode "Bloodlines", but was replaced by James Arnold Taylor for the finale.
On a more minor note, the Tribune in the Rimbor court was voiced by Miguel Ferrer in "War", but he was replaced by Nolan North in the finale.
Young Justice: Legacy sees Cree Summer (Aquagirl) replace both Miss Kittie and Denise Boutte as Rocket, Eric Lopez (Blue Beetle) replace Danny Trejo as Bane, Vanessa Marshall (Black Canary) replace Sarah Shahi as Killer Frost, Jason Spisak (Kid Flash) replace both Dave Franco as the Riddler and Logan Grove as Beast Boy, Kevin Michael Richardson (Green Lantern) replace Dee Bradley Baker as Blockbuster, and Danica McKellar (Miss Martian) replaces Alyson Stoner as Batgirl.
Screwed by the Network: In the US, Cartoon Network took over a year (January 2011 - April 2012) to air the 26 episodes of the first season (not counting a two-episode preview in late 2010). Other countries even finished airing them months before the US did. In season 2, the entire DC Nation block got bumped to January 2013 with no warning near the start of October 2012, when it had only run for two weeks. So that's two back-to-back, three-month-long hiatuses with only two episodes aired in between. This also affected Green Lantern: The Animated Series, and what's worse, none of the creators were told. They all found out from fans on Twitter. Even DC Nation itself wasn't told; they updated their official Facebook asking how viewers enjoyed the block, and ended up having to delete it after it was swarmed by confused and angry fans. The episode was released on iTunes the next day, and peaked at #2 on their sales charts before being pulled, and no one knows why. Both shows will be replaced by Beware the Batman and Teen Titans Go! after finishing their seasons. Any explanation for that either? Nope.
The leading theory is that this happened because the shows, despite being among the highest-rated on the network in total viewers, were struggling in CN's target demo of 6-11 year olds, along with toyline issues (GL never had a toyline, due to the box-office failure of the live-action movie leaving untold numbers of shelfwarmers in its wake, while Young Justice's toyline went belly-up after a few months in stores). The same issues appear to have struck down Beware the Batman, which (unlike Young Justice and Green Lantern) was just not popular in general. Sadly, Teen Titans Go!, by taking a different tack from the rest and playing straight into the Animation Age Ghetto, is now one of CN's highest-rated shows in 6-11 and is Adored by the Network while being hated by virtually anyone with some semblance of taste and standards.
Paul Dini revealed on a Kevin Smith podcast that the toyline was indeed the reason for the cancellation. To be more specific, the show had a large female and adult viewership, and the network believed that only boy audiences were worth attracting because they were primarily the ones that bought toys. Kevin Smith responded by faulting the executives with cancelling the series "just because [they couldn't] figure out [their] job", pointing out that they had a large audience that would have been willing to buy merchandise if only they had considered selling something other than just toys.
Kelly Hu voices Cheshire, her mother Paula, and her baby daughter Lian.
Red Arrow and Guardian (both clones of Speedy/Roy Harper, according to Word of God) are both voiced by Crispin Freeman. This is played with in the episode "Salvage", where the now-retired Guardian is one of the people who confronts Red Arrow. And as of "Satisfaction" Speedy finally gets to talk with Red Arrow.
Phil LaMarr originally auditioned for Aqualad, though he later agreed that Khary Payton was the better choice for him.
Weisman has commented that Wonder Girl was declared off-limits too early in the development process to know if she would have made the final cut for the season one or not. For various reasons the character wasn't unavailable till season 2... after the five year time skip, so Wonder Girl II, Cassie Sandsmark, was used. Wonder Girl I, Donna Troy, stands out as the only one of the Teen Titans' "Fab Five" not to have speaking part in season one, and so thus far the only one not to appear at all. Weisman laterrevealed that she had been part of the team during the timeskip and was actually intended to appear in the episode "Satisfaction", but the role had to be cut for time and budget purposes. She also would have used her later codename "Troia".
Mary Bromfield (as "Sergeant Marvel") and Freddy Freeman (as "Lieutenant Marvel") were two other timeskip members that were meant to have a role, but could not be fit into the season. Mary was also initially meant to be in "Satisfaction", and a story involving the Marvel Family had to be scrapped from the tie-in comic in favor of focusing on the five year timeskip.
The cliffhanger in the finale features Darkseid. If only this show hadn't been canceled...
In addition, there were plans to introduce the Wonder Twins, Zan and Jayna, in season three.
Post-cancellation, Greg Weisman, Brandon Vietti, and comic book artist Christopher Jones have been pitching various continuations, including TV movies, a spinoff show starring the Arrow family, an Earth-16 comic, and even a crossover with Scooby-Doo.
Both Icon and Rocket were slated for bigger roles during the "Invasion" story arc of the comic tie-in. However, they were written out after the first issue of the arc due to legal issues.
While it was never decisively settled on, because Cartoon Network only ordered 20 episodes for season two, Greg has said that if they'd been given more, there probably would have been an episode focusing on Zatanna.
Red Tornado also had an arc cut from the second season.
The little girl whose father Artemis saves in "Insecurity" was confirmed to be Cissie King-Jones— Arrowette of the original Young Justice comic book. Cissie would have become Arrowette in season 3.
Greg has also said that they had future plans for Ravager/Rose Wilson, Deathstroke's daughter, although he would have to do more research on her before then.
Furthermore, at the Young Justice panel in 2013, Weisman refused to comment on the status of things such as Darkseid or Wally's death, implying that there would have been future story arcs. The reason Weisman refused to comment is in the admittedly unlikely hopes that a continuation should arise.