I thought this was a duplicate of MC-858. However, reading through, this seems different, and is a bug I have been having since 1.8.9. It seems that a lot similar reports to mine have been redirected as duplicates to that issue, and I do not believe this to be the same case.

MC-858 is talking about blocks spawning/despawning as the server/client updates until they reach an agreement (And I am well aware of this old bug, I experienced it myself plenty of times). This, however, creates a permanent "ghost block" with different boundaries than a normal block. You can walk partially into it, and even damage yourself in the process. It will push you back like a mob. You can reload the chunks (fn+F3+A on Mac) and it will respawn as a normal block.. However, reloading the world itself won't remedy it.

I also went through the checklist of MC-858, and none of it seems to be helping in 1.9. When breaking dirt/sand it will visibly disappear, but it will repel you when attempting to walk through. Then, when a block is placed in the spot where you cannot walk through, and broken again, the block rebreaks and generates 2 blocks, one being the block placed over, the other being the "Ghost" block. I have been able to replicate this quite a few times. I even updated my RAM to 16 GB, and happens on both server (Realms) and single player. Through my testing, I found it almost always happens when at the edge of a chunk (will show 0 Y Z or X Y 0, or replace the 0s with 1s.). I am also playing on an iMac if that makes any difference.
These "Ghost" blocks also reappear if there is an update, like if the block was dirt and grass spreads to it. I have only noticed this happen since 1.8.9 myself.