Are the holes in the tube on the outside or inside of the tube. If it is on the inside check the rim tape and make sure all the spoke holes are covered, if on the outside it is something you ran over and also make sure the air pressure is at max for the tire used. You can get tires that have a kevlar belt for added flat protection, like Bontrager hardcase of Specialized armadillo tires in both road and mountain and run about $40.00 ea. If your tires feel thinner in the center than the out side edges they are worn out and need replacing.