Sometimes when breaking blocks, there may be individual blocks that appear to break but something still prevents moving over the spot where those were located. You may also take suffocation damage. I've seen this happen with dirt and gravel at least.

If you try to place a block into such spot, a block that was there previously appears. For example, dig lots of dirt quickly -> problem occurs -> place stone into the offending spot -> dirt block appears there.

Mining speed might have some effect on this but I'm not sure. This may occur easier when breaking blocks very fast, for example, with Efficiency IV enchanted shovel.