Holes in travertine are perfectly natural and are caused by hot springs or gasses passing through the rock. The pits and air pockets can be filled in the factory process, but these can pop out and come away from foot traffic when the tiles are first laid. Also, some travertine is sold unfilled and during the fitting the tiler fixer will float the grout over the whole tile and fill up the holes and pits with grout. This is perfectly fine, however the grout can become stained and discoloured if it isn't sealed and maintained correctly