I agree this is annoying. Playing as Ben Henderson wearing black trunks? What? He always wears white. I've tried pressing buttons and combinations of buttons but nothing. Just got to mirror them for now then cancel and pick your fighter.
Hellstorm here's how.
If you want Big Nog's alt and are fighting the comp then here's how:
Red Corner: Select any fighter, for the comp move him over Big Nog then press O cancelling your pick. Slide over to Big Nog and then you'll be using his alt trunks.
Blue Corner: Put the comp as Big Nog select him. Move your cursor to Big Nog. Press O to cancel the comps selection (your opponent). Select your opponent then you'll be on Big Nog with his alt shorts.
Haha ya, some of the trunks are questionable really. Example Dan Hardy's are black or white? Where's his traditional red ones? Ben Henderson fights in black but should be white (as previously state), idk what's up with Condit's shorts really haha. But ya I suppose that's how it is for this version.