It wasn't assigning the 3 npcs to the wrong consoles (they just take longer if you do). It was running to the airlock and boarding the Enterprise-C immediately after the last force field is down. If you don't wait for the others to catch up then "Saves More Than Nine" is incomplete. Log out then back in to try again.

When they catch up to you there should be a chime and "Saves More Than Nine" removes itself from the mission details screen in your HUD.

The only 'fix' cryptic should make IF ANY is to simply disallow the player boarding w/o the NPCs.