Blocks turn invisible when you break it with the wrong tool and when it is enchanted with efficiency 3-4. Ex:if you break sand, gravel or dirt with an enchanted pickaxe effiency 3-4 if will turn invisible and would not give the block. Also if you stand where the block was you glitch and you start making a movement like your jumping repeatly. The only way to fix it is if you place a block where the invisible block was at.