Your inventory became full during a Void Crusade mission, and since that time (even if you were to delete items from it so it isn't full anymore) specifically cortex fragments you pick up do not count as new ones in your inventory? Do you still have some, though, from before the inventory-full mission, only their number doesn't increase as you pick them up, no matter what? Am I getting this right? 

I assume from your text you have restarted the game several times since then, yes?
Could you please let me know what your in-game account name is?