I've been having issues with reactivation missions, but oddly enough not really with the mission itself. Once completed and it's time to leave,the settlements defenses target my SRV and my ship which I use to help clear out the scavangers/pirates. I think an old trespass mechanic is triggering while the permissions given via the mission in odyssey don't apply for the last step of the mission "leave settlement" if your not on foot. I can imagine this kind of mechanical issue is going to come up here and there, hopefully some other commanders can list some similar instances so Fdev can hammer it out a little quicker 