Same issue, and after checking several times I'm 100% sure I got everything.
Tonight I am going to all the planets, exiting to the orbital station, then exiting to the ship rather than going directly to the ship. Only thing I can think of.
**EDIT** I now have completed CH 3, all I did is what I described above. Go to all the CH 3 planets, then exit to the orbital station, then to the ship, do not exit directly to the ship