I costumed a bunch of ground units, and occasionally I see their original name over their head, presumeably because they spawned a type of unit at random for which there's no equivelent title in the costume's race. But the costume always appeared.
If I renamed all the single actors correctly, I never saw that so far.
What can happen of course is, at some levels e.g. Klingons will come alongside their beautiful Targ and Gorn with their attack Saurians, which belong to a handler NPC.
It WILL look weird to have the Federation attack you with these animals, of course.