I have happens one problem
Bot on maps often kills the boss or rare, then collects some loot and goes to the town, sells and returns to the map.
Next, he picks up 1 or 2 remaining items and go back to the city, although the map has not yet been passed.
As a result, he often uses portals and sometimes not even finished the map because he spend all portals.
sorry for my english
Maybe that's beacuse you pickup all rares? I fixed clearing map 100% by picking up only rares 2x2 + staffs (or 1x3 if u want).