When using an efficient shovel while mining, all target blocks seem to disappear, but an invisible block remains, keeping you from moving forward. Logging out and back in reveals the invisible block, which can then be mined. If you place a few blocks of any kind in the approximate area, that block will be replaced by the errant block (usually soft mats like gravel/dirt.) Doesn't seem to happen while breaking hard blocks w/a pick.
Related issues
duplicates
Comments

Actually duplicate of MC-5694
Duplicate of MC-858.