The following article contains spoilers from Dark Crisis: Young Justice #1, on sale now.
Young Justice may be back, but they're not as united as they could be. After the death of the Justice League, Robin, Superboy, and Impulse have mysteriously vanished, leaving Wonder Girl to try and sort out what became of them. Looking into the pages of Dark Crisis: Young Justice #1 (by Meghan Fitzmartin, Laura Braga, Luis Guerrero, and Pat Brosseau) it becomes clear that there was a fundamental difference in the problems Wonder Girl faced when compared to her friends.
The boys have been trapped in a world more suited to their desires, one which they considered a happier time in their lives. Unlike them, Wonder Girl did not pine for a time that was long behind them. Cassie's problems were focused more on the here and now. As such, it seems logical that she would not have been put in this prison because it is not what she desires.
Even her assessment of her friends, as harsh as it may have been, pointed out that all of their problems stemmed from their past. Wonder Girl on the other hand, was more concerned by the problems she was facing now, as opposed to the problems back then. The murder of Queen Hippolyta and now the loss of Wonder Woman has embittered her to her present situation, but it hasn't made her long for the past because she recognizes how toxic their behavior was back then.
The boys on the other hand, have not made this discovery and still silently wish for things to be simpler, when in truth, they never really were. This is the difference between them and her: Wonder Girl has moved on. She is living with the present, and as such has learned from her past. The boys have not, and as a consequence, whoever took them has placed them in a prison they will not be inclined to leave willingly.
Further support for this theory is that Cissie, or Arrowette, as she used to be known, was not taken either, despite being a former member of Young Justice. The key word here is "former" Cissie hasn't seen her friends since Young Justice was first reunited. Since then, she had been applying to various colleges and moving on with her life. She adamantly refused to join Wonder Girl's investigation to find the boys because she didn't want to be a part of that life anymore.
Though she didn't elaborate why, it is clear that Cissie sees how destructive being a hero can be, and has no further desire to be one. As such, she alongside Wonder Girl were excluded from the vanishing of Young Justice. Both young women simply did not believe the past was as great as their other friends do.
This may also explain why wherever it is Young Justice has been trapped has its own version of Wonder Girl. Since the real one does not want to be in the past, had she been trapped there too, she would have fought the hardest to escape. To compensate, this prison that Young Justice are in created its own Wonder Girl to allay its occupants' suspicions, or at the very least, distract them with a Wonder Girl who does want to be there.