Hard to say exactly because I can't see the problem well enough to say for sure what the fix should be.
Osmotic blistering is usually the result of prolonged immersion is warm water so I wouldn't expect that is your situation, but never say never
There can be two other kinds of defects that look sort of like blisters. One is swelling caused by a caustic chemicals. Don't ever try to clean stubborn stains with something like oven-off
The second is a hollow void with a thin layer of gelcoat over it that may or may not break and look like a popped blister.
I wouldn't be concerned about whatever the exact situation is. Either way it's not a big deal.
Since you're going to reseal the window anyway why not post a close up photo of the area when its cleaned and exposed so that we can give you more specific repair suggestions.