Hello,
I have uploaded two saves (link to this post in both), one where the quest does not fail but no rep gain for defending the caravan, and the one where it fails stating I attacked the Caravan. After further testing the only difference I can recognize that may have an effect between the two saves is the attacking and defending team changes.
In the save where the quest fails, the Caravan is the attacker and the Looters are the Defender. In the save it does not fail on, it is the opposite. My previous conclusion regarding alt+left click to escort doesn't seem to have an effect afterall.