Are the holes all in the same spot on the tube?
If so, line them up against the wheel and look verrrrrrrrrrrrrrrrrrrrrry carefully around that area. Check for any burrs on the rim itself.
If they're always in different spots, you might be up for a new tyre. I think Contis have two little dots that act as wear indicators which tell you when to replace your tyre. If you can't find the dots... well.. there's your problem