Hey I just joined up to get help with this!

I had Boone as a companion when I went to Cottonwood cove (after getting the pardon from caesar)

Everyone there was already dead from an earlier visit but Boone immediately killed the guy at the barge, and now I can't get to the fort! There's no way in around the cliffs, I did a LOT of swimming. Does this need to be patched? Do I just need to start a new game? What can I do?!

You can still get to the fort by standing on the barrel raft, looking down and hitting X to enter "The Fort," but without talking to the guy on the pier you cannot progress with the quest. Boone will not let you do that quest anyways, as he will kill on sight all Legion troops.