Bella was confused by the way that the Watcher spoke. It wouldn't make sense for them to betray her and Connor like this just because Luke was in love with her. In fact, by the way, the Watcher described it they wanted Luke to fall for Bella and for them to end up together.
"Why would you care whether I ended up with Luke or not? I helped you just as much as him when I met you so it wouldn't make sense for you to go to these lengths." Bella questioned in anger as she didn't understand the reasoning much less believe whatever the Watcher was saying.
After these words left Bella's mouth even Luke seemed a bit confused as he thought about everything that had happened so far to himself. He seemed to be questioning the same thing in his mind but decided not to say anything since they are on the same side.