It's not just that mission; there's a few of them that glitch that way. It usually fixes itself if you play again, but sometimes it won't work unless you wait a few hours.
Usually what causes it is when the mission somehow allows you to skip an objective (or you miss a hidden objective like "kill all the Orions on the planet in "Divide et Impera"). Sometimes the objective will even be glitched and never appear in your mission tracker.
If it doesn't repair itself within a day or two, you might have to send a game ticket.
One thing that sometimes helps is to check to see if you can turn in the mission BEFORE you warp out. I replayed "Doomsday Machine" last night and even though it gives you a "leave system" prompt, you can turn in the mission immediately for the rewards. You don't need to leave the system to collect.