1. The lumber, studs, that the drywall is nailed to has moisture within it, as the lumber dries it shrinks and this shrinking is not uniform on all boards or even throughout any individual board.  When the board shrinks an air gap occurs between the drywall and the stud and if something or someone applies some pressure against the wall, it will close the gap and the nail head will appear!

The use of steel studs avoids nail pops completely.  For two reasons.  Steel studs do not shrink or warp and drywall on steel studs must be installed with screws.

2. If the drywall is not pushed tightly against the studs or roof joists, when the nails are driven in, a gap could be left between the structural member and the drywall.  Again applying some force to the drywall will make the nail head appear.

3. Gaps between the drywall and studs or roof joists can also occur if the contractor skimped on the number of nails, when doing the installation.  It is not that nails cost a lot, but the labor to install them does.  If an installer uses 20% to few nails they have saved 20% of the time required to nail the drywall in place.  On a single home this can equate to man days of saved labor.   One reason to always be suspicious of a very low bid.