As a former bodyshop owner who has gone through 100s of gallons of filler, I will say that it's almost certainly rust in every case. Filler is a lot more forgiving than Jim's experience may indicate and a tiny air bubble will not necessarily manifest into a bubble. Poorly cleaned or improperly repaired metal is perhaps a secondary cause. Brazing flux residue is notorious for causing bubbles and most good shops will remove any found brass these days. A third possible cause is improperly mixed filler, but there is such a big lattitude in the mix ratio that you have to get it really wrong to cause this. Moisture trapped in the filler, poor paint prep or adhesion are yet other possible causes.
If you're going to repaint and change color anyway, you might as well start saving your money for a complete overall. I would find a shop you like and get an estimate so that you can begin budgeting.
