Seems like there may be a bug near the end when the Pelican arrives to extract you. An ODST jumps into one of the seats causing Master Chief to not be able to get into the Pelican, only by killing that ODST in the seat is Master Chief able to get into the Pelican and sit down so that the Pelican can fly off.
For context, this was tested in coop with 2 people

Seconding the above bug report.
I ended up with the same amount of surviving ODSTs as available seats in the Pelican (Heroic, Singleplayer if it helps) and even though there were still 4 empty seats, 4 of the ODSTs wouldn't load up and I couldn't board the Pelican myself to end the mission.

No good deed goes unpunished.... Chief only has animations for 2 of the seats in the pelican, so that's probably what's causing this. I'll look into it! May be able to script it so ODSTs can't sit in those seats