Invisible block can't stay when you dig very fast. For example when you use diamond shovel with Efficiency IV or V to dig the groung.
When you save game and load, the invisible block now is visible.
This problem start after Minecraft 1.9.
Linked issues
duplicates 1
Comments 3
Duplicate of MC-5694 – If you searched the tracker before creating this report, and were unable to find the indicated ticket, please comment with the keywords you searched for so that the original report can be improved.
Looks like MC-5694