its the way the game was set up from the start. im sure it wont get changed now as its technically too much work for not much return.
when you fight a klingon enemy the game sends you up against either the klingons, the gorn, the orions etc. they are not mixed groups. they are one mob of that species with their individual powers and stats.
with starfleet you are seeing the diversity working together as one unit, so when you kill them you are killing starfleet. the appearance of a ferengi, a bolian, a bajoran is just cosmetic and often generated randomly for the mission.
it would probably look a little odd to just face a group of 5 bajorans or 5 bolians, or having a diverse group of 5 enemies of different species would require 5 different mobs of 1 rather than 1 mob of the same 5.