Adding item to shulker box

Occasionally when I add items to a shulker box, the item goes into the box but creates a "phantom" inventory slot that can't have anything else put in it. This happened with 6 bones in my toolbar. Upon scrolling to them on my toolbar, the 6 bones pop up even though I supposedly put them in the chest.

 

A second time, a slightly different issue happened where the 6 bones could not be moved from my inventory to anywhere else, and I could not place anything on the stack - again after/as I added stuff to my shulker boxes.

 

I noticed this occurring yesterday but didn't think anything of it because of where I was in the world (lots of redstone in that area).