I have been noticing that the looter is not deleting the bookmarks after it is done with the site. What it does is dock back up unload the cargo then notices the bookmark and go to it again. It will delete it now as there is nothing to loot. This can be time consuming if it has to do 3 or 4 jumps away from station.

Another thing I have found is if you do a bookmark in the last stage of a mission the bot will warp and hit the first warp gate. instead of looking for the gate it keeps trying to warp to the BM but it can't because of the 1st warpgate. If I BM the first gate it works fine.