the way water blisters are done is by storing in the water at least for many days if not a part of the season. also if for some reason there is a pin holes in the gel coat. a few boat companies over the years has had this problem do to a number of reasons, ranging from wrong mixing of gel coat to not totally cleaning molds. under the even new boat warranties it may or may not be covered, you really need to check as most will not warranty the gel coat. you can take it to a glass shop and have them look at it. it usually is a pretty common occurance with boats that spend say a summer in the lake/ocean, sail boats, runabouts and such. Not as often in bass boats. but it has happened in at least 1 manuf I know of and they fought tooth and nail about fixing the problems as it was not just one boat but quite a few.
I do want to ask this also is it where your bunks hit the boat Or really close? if so you may have too heavier carpet on the bunks that holds the water longer than the normal bunk carpet.