Yeah, I found that quite disappointing. You walk in to see the hirogen and Klingons fighting, only to discover that both are still considered your enemies. It seems like they'd want to team up for mutual survival. Worse still was at the end, after you bring the force field down, the Klingons you just rescued are standing around on the other side of the map and quite willing to shoot at you if you stray too close.
It's ridiculous. Nothing like that ever happened in any Star Trek episode to my memory. The whole point to being stuck in an anomaly with an enemy was to force them to reconcile. If they didn't, they ended up wiping each other out. There was a message in that. Ironically enough, this game by a company called "Cryptic" can't even understand the subtle messages the series contained.