You need to use an different finisher spot putty to fill in the small holes. I have a tutorial on my site:
ok does anyone have any tips on filling in holes in hardened bondo.
im so close to getting my civic dash done but everytime i sand it down i always uncover bubbles and find myself mixing more bondo to fill it in.
It is necessary to mix the bondo correctly in order to eliminate bubbles (which are the cause of pinholes). To do this you want to put the bondo and hardening agent next to eachother on a flat surface (I use a piece of cardboard). Then to mix the two you want to do a pulling back motion with your puddy knife. Pull the two substances down together and make sure you are pushing down with the knife. This will push all the air out of the mixture. Doing this in your preliminary bondoing will eliminate further work needed to fill in pin holes.
also some of the higher end lightweight fillers are better at eliminating pinholes, such as rage gold as opposed to bondo brand, etc.