Not sure how and why it is happening, but anyway.
Quite often when you start killing mobs and have magnet in your inventory not all items can be seen in your inventory( after a while when inventory gets full and everything is dropping on a ground seems like you still have some empty slots in inventory but in fact it is occupied by invisible items), you can see/sell them them only after relog.
Same thing sometimes happens when crafting in manual craft as well.( craft - nothing in invenotry , relog you got the item )
Quite often when you start killing mobs and have magnet in your inventory not all items can be seen in your inventory( after a while when inventory gets full and everything is dropping on a ground seems like you still have some empty slots in inventory but in fact it is occupied by invisible items), you can see/sell them them only after relog.
Same thing sometimes happens when crafting in manual craft as well.( craft - nothing in invenotry , relog you got the item )