Inclusion of air bubbles in body filler usually means the filler has been poorly mixed, and/or poorly applied to the car. Ie air has become trapped in the filler when mixing the filler and the hardener. A few days or weeks later the trapped air can shrink or expand depending on hot cold etc.
Best to use a wide flat scraper on a large flat clean piece of sheet metal and use wide flat motions to mix taking care not to trap air in the mix. Mix until the filler is of uniform colour. Obviously also be careful when applying to the car. When you get the knack of his process it takes only a few seconds to completely and reliably achieve 100% mix.