I lost a Critical HS because the Trident was frolicking around somewhere else
instead of shooting the Queen. So I had to do it myself but at 6% the HS was
lost. But since I was already there I killed the Queen anyway. When I docked
at the station the mission was back and when I took it the sector was empty.

Aw, this bug was supposed to be fixed as of 1.8.143. Apparently not then

There were numerous topics on this, but the most relevant one seems to be this one:
http://www.vendetta-online.com/x/msgboard/2/22751