Lots of possibilities here. The body filler and primer both need time to "out gas" before subsequent paint layers. Are the bubbles between the filler and the primer or between the primer and the color coat? It could be a chemical rejection between non-compatible filler/primer/colorcoat. Or, there may have been contamination by a foreign substance like oil in the air, silicone, even fingerprints.
Contamination on the surface.
Overmixing of the filler, getting entrapped air bubbles.
On a second (or higher coat), sanding the suface, having powder remaining on the surface, and layering another coat over it. Making it worse, sanding it down until the top layer is paper thin in spot, and it releases from the other Bondo surface.
hee hee, the applicator is usually to blame. stupid applicators puttin the stuff right overtop of rust spots and rusted out holes in teh car. people shoving rags and crumpled up newspapers into the hole, and then laying on the mud. some applicators are really ignorant and create panels that don't really exsist, with only a few gallons of bondo.
the type of bubbling I think you are referring to, is rust. I have fixed lots adn lots of rust spots on cars with body filler. I tell people, "this isn't gonna fix the problem, it will just hide it until it gets worse." You know what people generally say? "Oh, I am gonna be getting rid of the car in a couple months anyhow, so, just fix it cheap." Then, wouldn't you know, 8 months down teh road, I get... "Hey, my car is getting bubbles in it, you didn't fix it good." That's when I say, "YEp, you are right, I didn't fix it good, you didn't want it good." I get some people who hmmm haw around, and others get downright nasty to me. sonsawitches...
Yep, the metal has to be super clean, especially if there is rust in the area. The hole has to be patched. You got to get rid of all the rust by grinding or replacement of the metal. MEtal as it rusts EXPANDS so it will pop off any top treatment or repair.
As with any metal surface in contact with plastic (an insulator) The drip point for moisture will be between the metal and the plastic.
I always put on a coat of junk primer prior to putting on bondo. That way the metal is coated with a material prior to putting on the wet stuff. Bondo does say it is good for over painted or non-painted surfaces, so does seam sealer.
But the most important step is to make sure moisture and humidity cannot get into your repair. Sealing both sides of the repair with (back side with) seam sealer and a good coat of an epoxy or sealing paint (on both sides) is the best bet. It locks out moisture.
What! don't you know the customer is always right when they come back with a problem!...hey,hey...just kidding :: Thought you might need a little laugh this morning, John...
Ahhhhh, don't sick Dave on me...