The white flecks that show on the face of the rug are actually the untrimed
ends of knots in the warp strings. Weavers don't always use continuous lengths
of cotton string as the warps--sometimes they tie together shorter lengths to
make a warp long enough to string from loom beam to loom beam. Often the weaver
doesn't trim the ends of the knot in the warp string closely, relying instead on
the eventual thickness of the rug's pile to hide the knot and the ends of the
knot. When the pile of the rug wears (to perhaps half its original thickness or
less), the end of the knot in the warp becomes visible as a white tuft on the
face of the rug.
Sometimes the pile of the rug has worn so low that even the ends of the warp
knots have worn away, and the actual knot in the cotton warp is exposed. The
warp knots appear as small round, hard white nubbins sprinkled in an area of the
design where the pile is quite thin.
There is an easy (though time consuming) fix for this problem. Using a small, sharp sissors, you can open the nap of the rug at the white fleck and clip off the end of the knot in the cotton warp as close to the base of the rug as possible. This doesn't damage or weaken the structure of the rug, it just gets rid of the unsightly white flecks in the design. The downside is the time it takes to clip all of these flecks, especially in a carpet-sized rug. This can be an expensive undertaking if you have a rug dealer do the work, as it can take hours and hours to clean a large rug of white knots.
Oriental rug dealers sometimes are unwilling to go to the time and expense to clip the white knots from the face of a rug, preferring instead to touch them up with colored markers. This is not a good long term fix. The marker color can lighten or even disappear if the rug is washed. Even if the marker is colorfast, coloring the nubbin of the knot still leaves the knot itself which looks different from the surrounding pile.