Are we talking inside or out

As a decorator of about 30 years experience, I have had this happen numerous times. Its normally contamination, and the usual thing is lots of little seperation craters.
Clean down with white spirit and thoroughly dry off. If it repeats, get a small tin of Primer/Sealer, or a B-I-N sealer (Shelac based....be very careful as it sticks like sh1t to a blanket.)
If doing outside...I personally never use water based paints. Although expensive, I have always used Dulux Weathershield, but they have changed the formula of that , and I don't think its as good as it once was.

Oil based paints are imho far better than water based acyllics etc. Water based products allow bleed through of many contaminants, especially nicotine, and yellow much quicker than oil based paints. However, under the right conditions, Acryllics can be a boon for inside undercoating, allowing undercoat and glossing in one day.

I would think the most probable cause of your problem, was the delay in top coating.