As of "Misplaced" from Season 1, Young Justice has officially become a Saturday Morning Cartoon as part of the DC Nation Block. Granted, Saturday mornings on Cartoon Network aren't too kid-friendly, but some of the stuff the writers of this show get away with on the show is so jarring that one has to wonder what actually got cut. Of course, given how the show is apparently marketed with teenagers in mind as well...
Miss Martian's bioship has an oval shaped opening on it's base when members of the team need to jump out. Then she mentions that the ship is female. How did the censors not notice that?
"Schooled" has Wally in a sparring match with Black Canary, where he tells her he'd like to show her some of his "moves." His tone and facial expression make it very clear that he is not talking about fighting...
From "Bereft", pretty much any scene with Artemis and Wally got crap past the radar. But let's start with when the Team is suffering from amnesia and Wally had just found the button on his chest that changed his suit from the flashy red and yellow palette to the stealth black palette:
In "Happy New Year," just after viewers find out Miss Martian and Superboy broke up, they find Miss Martian with a new guy making out...for at least 20 seconds in the background. This may not be too big of a deal, but cartoon characters normally kiss for about five seconds, ten seconds max. Twenty is a lot, but the writers got away with it.
In the episode "Salvage", Wally comes home on Valentines Day to find Artemis, shown above, wearing nothing buta T-shirt (given that he's taller than her now and the shirt covers everything, it's almost assuredly his). C'mon, writers, that's not even trying to be subtle.
This line from Jaime. They could have said kissing or even cuddling, but they leave it up to the viewer's imagination.
Jaime: I know you just took me because Gar was studying and La'gaan and M'gann were whatevering...
When Green Arrow is trying to convince Roy to side with him again he says "It'll be just like old times. You and me; fighting crime, hanging out, shooting the-" before he's interrupted by Roy.
Jaime's subplot in "Beneath" is an extremely non-funny example: heavily implied Domestic Abuse. On a kid's show. Maurice's constant aggressive body language, Shelly's insistence that he "has good days", Tye's determination to get the hell out of that house...
Shelly: Don't mind Maurice. He's having a bad day. Jamie: I hear he has a lot of bad days. Shelly: Good ones too, occasionally...
In "Depths", when Superboy talks about why they broke up is very unsettling, the way he puts it is like he's talking of actual rape
Superboy: After all that we've been through... how could you think I wouldn't recognize your touch inside my mind? Didn't you know what that touch meant to me? And to have you pervert it like that.
Artemis: The more impressive trick is how got something so specific from Zatanna without revealing who or what it was for. Nightwing: We have a history. Wally: Dog!
Speaking of Nightwing and ladies, issue #20 of the tie-in comics had him videochatting with Wally and Artemis in his pajamas. Then Bette Kane in a tiny black dress walks in. And if the comic itself isn't clear, Greg Weisman's note cards clearly state that she entered from the bedroom. And Chris Jones' original pencils showed him shirtless, with the door to the bedroom open and the bed unmade.
Bette: Morning, uh..."Handsome" Wally: You dog! Artemis: Oh my God!!! Is that...??!!
On Wally and Artemis's end, they were up at 5AM doing "Physics" work. Artemis even mentions that she's always up that late/early.
In "Satisfaction", Conner asks Mal what everyone is up to:
Mal: Well, the girls are at the shower.
A later scene reveals that all the female members of the team at a bridal shower.
During "Before the Dawn" Black Beetle pins Cassie to the door, and traps M'gann halfway through the door by shifting its density while she was going through it. The following conversation is disturbing to say the least-
Black Beetle: "Wasn't quite prepared for that, was she? But don't be jealous. I can put you halfway through the door too. Halfway... the HARD way."
He then starts BANGING her against the door (and we all know what that's slang for) as she grunts/yelps with every smack.
It is surprising that they let a beatdown that long or brutal happen. It's ten seconds of slamming a young girl against a metal wall until she loses consciousness. And not in the Hollywood way, in a "severe trauma" way. Probably the reason they flashed through the teammates at that moment was to let that through.
In issue #21 of the tie in comics, Scarab notes that Cassie causes "biochemical reactions" in Jaime and he should not trust her.
In "Cornered", the radar fails to notice a description of Cold-Blooded Torture and the implication that God knows how many kids were murdered by the Reach.
In "The Fix" Impulse saying to Blue Beetle "the night is young"
Also in "The Fix" M'gann having suicidal thoughts is no-so-subtly hinted at. She's so wracked with guilt over destroying Kaldur's mind that she lets the "Tula" she finds in Kaldur's mind attack her viciously without defending herself, saying that "it's [her] fault."
When he sees Bumblebee and Guardian kissing, Arsenal wonders why he doesn't get that kind of reward. Wonder Girl gives him a peck on the cheek.
Arsenal: It's a start.
A much darker example later on, when Arsenal gets so desperate to not become a prisoner of anybody after his five years on ice, that he actually tries spacing himself alongside the rest of the team and the Brainwashed and Crazy Blue Beetle. That's right, kids, a murder-suicide that would have taken all of his friends, had he succeeded.
Yeesh, no wonder Nightwing kicked him off the Team!
The final issue of the tie-in comics heavily implies that Marie Logan, Beast Boy's mother, is a lesbian or bisexual. Queen Bee uses her mind control/seduction powers on her to make her commit suicide.
There's also the ending where Barbara meets with Dick at a Blüdhaven warehouse at night. Two teenagers who like each other meeting at an abandoned warehouse after midnight. Alone. Do the math.
Artemis delivers another gem:
Wally: I so wanna kiss you now... or maybe kill you for putting us through all this. Artemis: Hold that thought. You can decide later... when we're alone.
There's also a surprising amount of blood, though certainly less than there should be. Ra's al Ghul gets stabbed through the chest (he'll recover, but still) and has a blood stain from the exit wound, Mallah visibly bleeds when Beast Boy bites into his shoulder, and both Artemis and Kaldur get shot in the chest (though those were faked).