The last few cakes I've made I've used MMF, but both times, large bubbles have formed UNDER the fondant (between the cake and fondant) after taking it out of the fridge. I tried using a pin to get the air out, but by then, the fondant had stretched and it was ruined! Anyone know why this is happening????

I've had this happen to cakes that were refridgerated then taken out and in a spot for a prolonged period of time that is too warm for the cake to be in.
I've been able to poke them and pat them back in place luckily, but I believe it could possibly be caused by the buttercream underneath (if used) sort of melting, or just simply air that's being let out of the cake itself.
Try letting your cakes "rest" for a period of time before decorating (I let mine rest at least overnight, sealed in the fridge). And of course be sure to tap out air bubbles after pouring the batter into the pan.
HTH

I had the same thing happen for the first time recently as well. I was told that it was likely because I iced my cake frozen, then put the fondant on when it was too cold. But I always do this and have never run into a problem.

I think it was more likely Spills explanation - not enough 'settling' time. Give your cakes at least a couple of hours to settle.