When the autosell did start happening for me I was able to chase down where to control it from. Go to your Buy/Sell screen and you will see a small symbol box down the left hand side beside each item. If it is a checkmark, any of those items loose at the end of a mission are automatically sold. If there is an x, then the items are transfered into your inventory. Click on the icon to be able to change it from the check to x and back again. Note that it seems to default to selling most of the researched items but not your starting types of equipment.
Brett