I seem to be having this issue but I did not realize it was happening because of food and drinks. I just find that some inventory slots become unusable even though there is nothing there. What I do is remove the article of clothing onto the ground and pick it back up (of course as long as it doesn't disappear through the floor haha!). Then the inventory slot is usable again. I was going to open a new issue for this but I think it might be related to this bug report.
May 10 2016
I can confirm that after my friend disconnected, I handcuffed them and the character disappeared even though I was rummaging through their inventory.
Thanks iBane! When you put it like that it does seem to make sense that it is working as intended.
Thank you for the added note. However, I feel this is a little different than the other post someone made about logging out AFTER they have been handcuffed which I agree the character should be reset. This is an issue for being handcuffed AFTER the player has clicked the disconnect button. It originally occurred due to friends messing around with handcuffs thinking the person would just log back in with the handcuffs on. This could be used for griefing though. You see someone logging out, or know someone is logging out, you can quickly run up behind their character and throw handcuffs on them. This will force them to respawn with no gear and they would have no idea as to why this happened because they disconnected from the server with no issues. I am not sure how this should, or even could, be fixed / changed but I just wanted to make sure the devs were aware this could happen to someone AFTER they have disconnected from the server.
Can confirm this happened to me today. I noticed yesterday that my inventory in my 35 slot backpack had been rearranged but it didn't effect my shotgun. Today, my inventory was rearranged again but this time it did put a bag of rice over where my shotgun was and the shotgun was nowhere to be found.
Can confirm this is happening on current stable build, I have heard if you move the box to a different bag or to your pants or shirt or just someplace other than the bag where the partial stack is, then empty the box, it will be okay BUT I have not tried this myself.