Here is a write up I saw about 10 or so years ago, so some of it may be outdated??? It was written by someone called "Overspray" on some other forum. The bubbling does sound like a moisture problem to me, and a lot of guys lay this stuff on too thick, it leads me to think its operator error, and not a 3m problem. "Overspray" also addresses pin holes, here is what he had to say about fillers.
"I use to work as a technical/sales rep for the company that makes rage filler. I know the guys (chemists) that developed the resin for rage filler. I've been a bodyman/painter,sales rep and technical rep for 30 years. The resin in rage and other body fillers is fiberglass (polyester) resin. Today's resin technology makes the adhesion of these new resins as good or better than most epoxy adhesives (glue). They are designed to really stick! Most critical is to be clean and moisture free.
Body filler resin is a thermal set plastic-it cures with heat. The hardner-MEK peroxide is a catalyst that produces heat in the resin. It needs to be at 64 degrees F minimum, to cure-best is 72-80 degreesF. If the metal is cold the filler will cure from the outside in and could trap some moisture and solvent from the resin underneath-causing adhesion or bubbling problems later. (Styrene is the solvent in resin and produces the smell/odor we associate with bondo and fillers). Also moisture (humidity in the air) will condense on the surface of the cold metal. This is the same effect you get when the mirror in the bathroom fogs up when you shower. The mirror and the metal of the car are about 10-15 degrees cooler than the air temperature and the humidity condenses on them. If you warm the mirror or the car metal to about the air temperature, the moisture won't condense on the surface. Using a heat source to warm the panel will eliminate the moisture being trapped under the filler (which can show up as rust under the filler) and help keep the cure temperature even through the filler, just don't overheat it. This is the way the chemists designed the product to work.
You can use extra catalyst to speed the cure, but too much will cause too much heat in the reaction and crystalize the resin which causes it to be brittle and break down (yup-more problems later). If you head to the autobody supply store for more hardner you may be using too much and looking at problems down the road. PreWARMING the metal and keepin the shop warm will let it cure more evenly with the correct amount of hardner. Heat lamps or lights should be far enough away so the panel feels warm when you put your bare hand on it (NOT HOT).
The correct amount of hardener is 1 1/2 to 3%. Here's an easy way to figure it. On the pallet or board you mix your bondo or filler on, put the amount you are going to mix up in the form of a circle. With your spreader or mixer divide the circle in half-50%. Divide the half in half-25%-half again-12.5%-half again-6.25% half again-3.125% (this is the maximum) half again-1.5% (this is the minimum). If you have a COLD shop put a small batch on a WARMED test panel to check the cure time-spread to about 1/4 inch thick. It should be fully cured in about 30 minutes to 1 hour depending on the temperature and hardner amount. (Yup, I know you can add a pile of hardner and get it to "kick" in a few minutes), but a good cure time lets the gasses come out and gives ample time to work out the air pockets with the spreader. (eliminate "pinholes") After a few times you'll be able to gauge the amount of hardner for the size of the filler batch you are mixing. There is some room here for a little extra-but not a lot of extra hardner. REMEMBER, this needs to work with the temperature of the air and metal.
Filler also contains talc (the mineral in talcum powder) which will absorb moisture. If you try to fill holes in a body panel, moisture can be absorbed from the back side and cause the area to swell and bubble. Also bare filler left in the weather (rain) for any length of time can absorb moisture and cause problems later. It will cost a lot less to follow these steps of correctly preparing the metal and working with the correct temperature range and hardner amounts than to even bother with epoxy primer as an underlayer. Between coats of filler DO NOT wipe with solvent (thinner).(Solvent will absorb into the filler). Rough up the areas not sanded and blow the dust off real good then apply a new layer. Thickness of the layers should not be more than 1/4-3/8 inch. If you put filler on too thick the heat in the reaction will be concentrated and higher in the thick area and could lead to crystalizing the resin in that spot making it brittle and subject to cracking later. Also too thick can mean you won't be able to get all the air pockets smoothed out."