I have the same problem but I have been using the iron with a sock on it. I have been sticking the covering to the wood whenever I get a wrinkle. This is on of the frustrating things about MonoKote and Ultra Cote is that they do not stay tight like when you first apply them. Years ago I never had this problem, but then I found I could make the plane look better if I only sealed it on the edges and then used the heat gun in the middle. I have come to the conclusion that the old way prevented wrinkles but gave lots of scratches and other blemishes.

I'm getting more particular about my covering job as I have gotten older, I'm giving serious though to going to glassing and painting my airplanes, even if it takes more effort, they will always look like they did when you finished them.

Andy