With a full inventory, items are unable to be auto-looted.  When completing a map in that state, the items are not sent to the scavenger.  If this is working as implemented, then I kind of feel like it shouldn't work that way.  If I was to go around and manually loot each of them, they would all be sent to the scavenger, so I feel like auto-loot should have the same outcome just less manual.  At the ends of the non-final wave, it would be ok for items to remain on the ground rather than sent to the scavenger, but again, in that scenario were you to manually collect them, they would be sent to the scavenger.