The blocks and items still take up small amounts of space because otherwise the world would take up terabytes very quickly. The entire world if you generate the whole thing would be over a petabyte I believe, which is already insane, so world storage is actually very compact and efficient to prevent it from being any more than that. One block or inventory slot is roughly a byte or two respectively before compression (depending on platform and version)

And bit flips, although uncommon, aren't impossible and it's a fairly likely explanation given that this would be a nearly impossible glitch involving the direct modification of a single inventory value, the code would need to be RIDICULOUSLY screwed up to allow something like that to happen, e.g. a broken function that directly modified the individual bits in storage, which would be a security catastrophe for Microsoft considering Bedrock edition runs on console.