Hardwood Filler is Popping up
Since it's almost winter now, you may have the answer just by observation. It's likely that if the installer said the wood filler would shrink back into the holes in winter, it would. But it will be ugly again in summer. There's also a good chance that foot traffic will break off the bumps where the filler pops up, which will leave you with pits when it shrinks back.

Another possibility is that the installer just gave you that answer because it would mean he doesn't hear from you again until winter, or maybe not at all if you've gotten used to the defect by then.

My solution for filling holes (mostly places near edges where I had to face-nail but didn't have space to hide the nails under baseboard trim) is to countersink the nails, then fill the holes with a mix of sawdust from cutting the floorboard material (so the color matches) and urethane clear-coat (which is roughly the same stuff my floorboards were pre-finished with). If your floorboards are finished with something else, you'd want to use that for the sawdust blend trick instead. Note that some kinds of finish will darken a sawdust blend; it's a good idea to test the blend on a piece of scrap before putting it somewhere people can see it.