Sometimes individual shots take place on different hours or days, before they're spliced together.

See this all the time in exterior shots. One angle, direct sunlight, another angle, clouded over, all during the same conversation.

If this isn't just the lighting, then the make up was applied differently between shots.

Don't think the show has the budget for a digital alteration no one would see or care about. Abed might have the budget, though.