It appears to happen when I manage to hit, say, a Lichen Colony with the explosion of a shard bomb and the shards from another at the same time. Suddenly, all the shard bombs I subsequently hit it with will make the invulnerable plinking sound and the enemy will take no damage. It can be resolved if I stop bombing for a bit so that the combo ends, completely removing any merit the bombs has. This is obviously due to the spotty manner in which the hard-coded limit that prevents more than 3 shards from the same bomb damaging the same enemy is made up.
I realize this is the bug report forum and not the suggestion forum, but honestly the limit should never have been implemented in the first place. Even if you were to hit a huge boss with every shard at the same time (and there's no way you could pull that off consistently), it would nowhere approach something like Blitz Needle and you should really just throw us bombers a bone here.
While fixing this issue would be appreciated, simply removing the shard limit would be the best for everyone involved.
Here is a video of it happening. On a tiny enemy, no less!
It's more broken than stun and disappearing shards combined.