I agree about applying fondant to a well-chilled cake; I won't do it any other way. Our house buttercream is Italian Meringue. (Your mileage may vary with an american style buttercream made with butter and confectioners sugar.) A room temp cake will be more likely to sag or change shape as you are smoothing the fondant in place.
When you are kneading the fondant, you can introduce air bubbles, and the best way to handle a bubble in the fondant is as Chefpeon suggests, to pin it as you are rolling it before you apply it to a cake.
If a bubble appears after you've put the fondant on the cake, it could be that the buttercream underneath is not as smooth as it could be. Even a tiny little gap will trap air between the buttercream and the fondant and if the weather is warm, the air will expand and cause a bubble to form under the fondant.
Definitely take care when applying and smoothing the crumb coat and see if that helps. Using a fondant smoother helps because it doesn't leave palm/finger marks and it applies even pressure.