I've found a few other threads on here for this topic, but I don't really feel satisifed I have an answer, so thought I'd see if I could lure some answers out of you all!

I just completed my first tiered, filled cake. I will detail my procedure, maybe someone can tell me why they looked perfect on the night, but 24 hours later all puffy and cracked where the air was trying to escape.

1) Baked, torted, wrapped, froze cakes.
2) While still frozen, filled cakes using buttercream dam & jam type consistencey filling.
3) Settled cakes for around three hours, wrapped in plastic to prevent 'sweating' on the cake, with something heavy on top to press it down
4) Full layer of buttercream, then into the freezer for ten minutes, or the fridge for longer if the cake was too big to fit in the freezer
5) Fondant

So far these are possible theories, I would love to hear more:
1) I used 1/2 icing-sugar and 1/2 cornflour for dusting my surface, and have since learned that cornflour/cornstarch can ferment under the icing... maybe fermenting produces gases which need to escape?
2) I think Sharon Zambito says something about moisture on cake causing this. I thought I had avoided moisture by keeping the cake covered while it finished defrosting, but maybe I didn't.
3) One of the other threads mentioned the cold being a factor, but a lot of people work with frozen or chilled cakes, and surely they would stop if they had continual blow-outs?

Something that has caused me problems with puffy sides is the fondant being trimmed exactly the same length as the cake at the base then when the cake defrosts, the cake settles and the fondant is now too long and it pulls away from the cake creating puffy sides. To aleviate this, I trim my fondant a .25" from the bottom so when it settles, it is about flush with the bottom, then any gap is covered with a ribbon or pearl anyway. I have also noticed that if I use powdered sugar icing, I get more bubbles in my sides than when I use swiss meringue icing. Hope this helps you!