My Instigate Defection completed while I was in another window. As did a Resettle Colonists.

When I tabbed back over the Instigate mission completely vanished without a trace.

Here's a screen showing the two previous missions claimed along with Instigate completing: http://i266.photobucket.com/albums/i...al/screen1.jpg

Here's a screen showing the Resettle completing:
http://i266.photobucket.com/albums/i...al/screen2.jpg

Where did it go?

Different bug - but my Instigate Defection completed with the Very Rare quality, but I was awarded a blue Doff.

"Very Rare" is the quality of the mission, not a guarantee of the quality of the reward. You can get a rare or very rare doff from completing the mission.

Well, I submitted a bug report in game and linked to this thread with the screenshots.