Ooh, a mystery!
It doesn't sound immediately familiar....
So the characters were a teenage hero group, but didn't wear costumes? Sounds similar to Runaways, based on the time period, but none of the characters had that power and I don't recall a scene like that, plus while Runaways was largely self-contained, it did sometimes have Marvel characters in there.
It's probably not Young Avengers, Teen Titans, Ultimate X-men or Young Justice, because they all generally wear costumes and are very much part of their universes, frequently interacting with mainstream heroes...
What was the art style like? Was it drawn in an American comics sort of style? Or more indie looking or manga?
Was it a print comic or a webcomic? I'm assuming print based on the period and you being a kid at the time.
Also, what country was published in? That's often really key, we've had a mystery solved in the past where it turned out it was a comic only published in Eastern Europe 