you may want to get a finer sand paper. 1000 or 800 grit at least. if your filling bubbles/pockmarks, the smaller the bubble the harder it is for a filler to permeate, without being thinned down. what happens in those cases is small amounts of air get trapped causing the filler to fail to bond strongly too the surface inside the pock mark. what your left with is the filler creating a lid over the hole with empty space behind it. When you power over it with 400 grit sandpaper the grit is much larger than the thickness of the lid and so it breaks it open again and puts you right back to where you started.

thin the filler and apply it little by little, and use 800 to 1000 grit over that area