Little pin holes that develop after a few minutes up to around 30 minutes after are called solvent pop.
It's caused mostly by spraying to thick of coat or while doing multiple coats without the proper flash time in between. Improper reducer temperature can play a part too.
Solvent pop is a nightmare. Not as much so with primer but with the topcoat is sure is. Nothing worse than having to sand off all your $300 per gallon paint. At least your primer was cheaper.
Yes, you are better off taking off at least down to where the pinholes are gone. Since you have solvent pop, you probably also have trapped solvents. And that's a really bad thing.