Spoon, saying what did you do to fail would help.
From fredwise point of view, im pretty clueless what problems you guys are facing.
I completed the mission without fail is all I did.
I'll have a look into your files in a bit, shouldn't be too hard to figure this one out.
OK, after replaying the mission, I know what went wrong. If you return to the Indigetes before the shuttle makes it, you fail the mission, even if you would have otherwise succeeded.
Oh, by the way, Murphy sends his regards. 
In my case, the shuttle made it way before I landed on the Indigetes.
Edit:
So I'm looking at stuff and I'm super tired right now so take stuff I write right now with a grain of salt as I ramble on.The BoardingNOOOPE mission objective has a redundant check in it. When you are checking if a ship has departed, you don't need the extra not is-destroyed-delay check. Because if the ship is destroyed before it can depart, freespace will automatically flag the has-departed-delay as false, since the ship is destroyed and can no longer depart.
And yeah, the shuttle has to dock (depart) before the goal becomes complete so you will fail if you enter the hangar bay before that.
The other reason why this mission result in a failure state despite the debriefing praising your efforts is that the BoardingNOPE checks if the RTB event is true, the RTB event is a distance check that immediately makes the mission end. So the goal doesn't have time to become true before the mission ends. Adding a simple extra event chained to the RTB with a 1 second delay and move the end-mission from RTB to the new event solves that.
Thankfully this mission was easy to check because it literally plays itself. No player input is required to achieve perfect victory. (You should definitely always check for these things for future fredding endeavors)