I have to agree with PhiloPhil. It's a minor gripe, admittedly, but it the fights in Defend the Sector mission feel like they are out of context until you hit the Terran Empire missions.
It's not unrealistic to think you'd encounter an enemy before knowing about them. The Enterprise encountered the Borg long before knowing what their MO was. Actually I think pretty much any surprise enemy that was encountered in any series were encountered as unknowns.