You can reproduce this.
Complete a mission with full inventory. When the overflow window opens, open your inventory, right click on a backpack to open it, so you can clear some inventory space, notice that it is full and open another one - the second backpack will overwrite the overflow window, with no way of recovering it. I've lost several tokens this way, accidentally.
Please make the overflow window a separate window, or do an inventory check upon leaving the mission area. If there is room in your inventory when you leave the mission, anything in overflow should automatically be put into inventory. This might be the easiest way to solve this problem programmatically...