If you try to sort weapons or tools with the three buttons on the right hand top, it will give you one of them into your inventory and one to your hand and leave the rest where they are.

How to reproduce:

1. Find a chest with more than 1 tool
2. try to sort them using the three buttons
3. get one of them into your hand
   attached are 1st unsorted and 2nd sorted using the middle one.

Confirmed... It occurs sometimes...

Duplicate #66
See my response there, issues of this type while sorting are fundamentally not resolvable on the client-side alone.