This happens to me every time on Orion Outpost. It doesn't register mission cargo escape pods.
how to reproduce:
find job in bar of the type "capture prisoner" (this may take some time)
fly out and do the job, return with the escape pod
land on Orion outpost, and you will be greeted with "mission failed, out of lives"
I recorded what happened: (original recording is in 1920x1080 but it was compressed and uploaded in 1280x720)
and here's another:
