Lovato told USA Today that the group has changed dramatically since they first performed for the judges in San Francisco.
"The thing is, they're not doing what we saw in this very first audition," she said. "It was an original song of theirs that I got stuck in my head.
"Now it's a little uncomfortable because they've become so manufactured. It looked like they were having so much fun. If [their mentor] Simon [Cowell] takes away their originality, it won't work."
Lovato added: "Staying true to yourself is the biggest advice I can offer to those guys. It's really easy to get taken down a path that you think is best for yourself when you have a lot of people telling you what it is."
However, Lovato suggested that Emblem3 will be "fine" after the show, whether or not they win, and praised their "charm".
"They're very cute," she said. "They've got the whole surfer boy thing going on. There's a lot of boybands, yes, but there aren't any that I feel have really, really strong vocals and a unique quality to them."
Cowell recently refused to say whether Lovato will return for The X Factor USA's third season, though he described her as "fun".
The show airs Wednesdays and Thursdays on Fox.
Watch Emblem3 perform 'Forever Young' on X Factor USA below: