Same issue here, I seem to only ever get them after I have completely killed an enemy. Then when I’m not in combat they spawn on the ground. I was wondering why I suddenly felt so squishy- it’s because I’m not getting any heals from it in combat.
It seems to be fixed. Check your game for an update. However, this is based on my limited testing and doing my WQs in Nazjatar. I was able to pick up all the lesser soul fragments that spawned.