Because you interrupted the collectors collecting everyone, thus at the end mission the collectors only get away with 1/3rd to 1/2 of the colony, and the closest to the ship were collected and loaded first. Ash/Kaiden were pretty far out, since everyone was running towards the shelters, which I assume is where the ship would land to speed loading of more victims in close proximity to the ship.
The collectors no matter their tech still need to load the pods manually.
that still doesnt explain why she/hes unfrozen b/c there are still sesker swarms