They had that sort of trouble years ago with fibrelass swimming pools. Lots of small blisters. In fact some ended up about an inch across. (2.54cm for the metricated)
I think it turned out that there were microscopic holes in the resin top coat and water was being forced in by osmosis, the same process that trees use to suck up water.
Real good for trees but not so good for swimming pools, surfboards or windsurfers.

Sounds like it might be something similar. The only way to stop it is to never leave your board in a wet bag. Otherwise you would need to sand off the original topcoat and re do it. That's what they did with swimming pools because obviously you can't leave a swimming pool dry.
I always leave mine in a wet bag because I'm such a caring and careful person with all my gear, not,( Borat not joke) and so far, no problems, so I think there's something wrong with your board.