Can confirm for 16w14a, 1.9.2, 1.9.1, 1.9 (that's all I tested)
Steps to reproduce:
1) Enter /gamemode 1
2) Place item into inventory but not hotbar (doesn't matter how items gets into the inventory).
3) Press q and drop item.
4) Open up a container (before it gets picked up if you're that close).
5) Inventory will still have item and item will be floating on the ground (or inventory will show 2 of the same item if picked up near the same time as opening a container).
Doesn't work with Survival or Adventure mode
Doesn't work if you reopen inventory after pressing Q but before opening a container.
Still affects 16w05b
/kill @e
works just fine on my end.
On the Steps to reproduce, it would be helpful to know if this was a previously generated world or if it was a newly created world (meaning, was it created prior to 1.9.3-pre1 or after).
I did notice it was a Flat world (bedrock, stone, smooth sandstone).