The tiny holes are in the grout because when it was applied, there were tiny bubbles in the grout. There are three items you need to fix this: grout, a silicone sealer, and a small drill bit. Spin the drill bit between your fingers to enlarge the pinholes before filling them with grout. (If you do not enlarge the holes, but simply apply the grout in the existing pinholes, you will have poor results.) Remove any loose material and apply the grout. Clean the surface and then apply the silicone sealer to make the surface waterproof.