There are a number of things you can try. First of all, you might want to clean the window once again. Sometimes, cleaning the window three or four times is necessary. Defrosters might also be the root of the issue, especially on back windows. You can sand down the defrosters or go over them with steel wool.
Another method involves turning the defrosters on after laying out the film. Squeegee out, then turn the defrosters off. The heat will cause the glass to expand, aiding in the tinting process and helping you avoid bubbles.