We had a new skim of plaster on existing ceiling, applied 2 coats of primer, and now flat latex paint and the ceiling paint is bubbling in spots, what can we do to rectify this.

Scrape it. skim it again.

wait longer for it to dry.

Your ceiling may have a higher humidity level than the rest of the room. Or you may have a duct above it that is producing condensation. Or something.

Could be a sign of a leaky pipe.

One can't tell without more info. But the skim coat probably just needed more time to dry.

Is it actual Plaster, or just a skim of Joint-compound?
* If plaster...one month of curing is often necessary. It's such a "dense" material, that water breathes out so slow.
* Joint-compounds obviously are ready much sooner.

Sorry it's not better news!
Faron