The single biggest issue I had was that:
Sending a second ship with you triggered all of my conspiracy theory triggers.
I constantly expected the second 'cargo ship' to become a gun ship (ie, it opens it's cargo bays and exposes it's missile launchers) kind of moment)
Because of that, I didn't role play as hard into the second ship as I could have, and always wanted to have a back up plan in case, even on the planet, they started to attack