@HopFrog I can confirm this problem. 

If I drop the 2nd of the 2 item stacks, it takes from the first slot to drop items and then starting to drop from the last when the first is empty. If you empty the first one without picking up any new of that item, you will get it to stack in one slot again once the first is empty.

The 2nd slot is usually the one disappearing when inventory is full.

Otherwise a fun game! :)

Im getting this bug too, could it be something in the way you store items or have them picked up. Maybe you have items go to specific spots in the inventory and when the original item shifts spots new items go to a different slot. Or perhaps the game doesnt pick up on the fact that there already exists an item of a specific type in your inventory. But the major effects of this bug that have hindered gameplay are that it will only count the stack the the furthest left in your inventory when it comes to making things, lets say if you have 40 wood but this bug happens and the left most stack shows like 2 wood. Any item requiring more than 2 wood cannot be made. 1 way i found to counteract it is to throw all items from the left stack until the entire left stack is gone then pick it up, it rejoins the right stack. This becomes a major problem if the left stack is huge for me i had over 200 gold ore in the left stack and 2 gold ore in the right stack. You cannot access the right stack and throw it. trying to put the right stack in your hand puts the left one there instead.  All of this becomes a major issue while there is no other way to store items. One other thing ive noticed is that if the left stack is small and you try to craft as  much as possible, it will access the right stack if the left is used up. This is as much as i know towards this bug from a couple hours of gamepay having to deal with it. I ended up having to fill every slot of my inventory so it doesnt happen and so i dont pick up useless items which i wish i knew how to sell them because i cant figure it out for the life of me. but I do hope that this knowledge helps you fix the bugs. Love this game i just hope you could t least add a chest or bigger inventory or a way to delete unneeded items since those are the only major hinderences to my gameplay experience