Heat blemishes occur when the elevated temperature causes the trapped air in the wood to expand. With nowhere to go, the expanded air causes a bubble to form in the covering and stretches the film. When the air cools, the stretched covering remains. You'll notice this happens especially with dark colors like black or dark blue, and that this never happens on the bottom of the wing, but only the top where the sun heats the surface.
The solution? While several methods have been tried—like completely painting the wood structure with thinned white glue to prevent the air from reaching the surface—we know of only one method of preventing this from happening: don't leave your airplane in the sun! Seriously, get a cover or a tent or find some shade. Also, choosing light colors will prevent the intense heat buildup. Last summer during our hottest days, I measured the covering temperature on a dark blue airplane that had been sitting in the sun at 163°. If you keep them from getting hot, there is no problem, but, for those times when they do, practice the re-shrinking techniques mentioned above, and it will only take a few minutes to bring back that pristine finish.