I have found that sometimes when I am mining, especially upward (ex: start mining some iron or diamond I find in the ceiling of a cave) that on occasion, an ore or material disappears after being mined (without entering my inventory). Once in a while I will find the missing ore on the surface of the land above ground, or maybe on the floor of another cave I find nearby. This applies to all collectable materials from cobblestone, to dirt, to wood from trees. (Do note, it doesn't happen all the time, but it does happen commonly enough to become frustrating).