Did you heat the patching compound to dry faster? Is this even a question are you asking can it happen? Or what to do about it?
Air bubbles happen for a couple of reasons, surface contamination or incompatibility with two different finishing systems.
I assume you already have the air bubbles so this is what you do. Scrape open the bubbles, prime with original oil base Kilz and let dry over night, apply topping as the final finish/sand coat. Topping is a little different than all purpose joint compound.
All purpose bubbles when put over hot mud, powdered setting mud.