That's the one where you've got to recapture the Clee-San right?
I've had this happen a time or two, I like HW:C better than the original you see. The way I fixed it was to redo the mission.
Failing that, go back to the autosave from the end of the previous mission. The script does get confused, but if it does it more than once, that means it's confuse from the start.
If you haven't already, assign each ship type to a quick key.
Strike Craft - 1(1 squadron of 10)
Multi-Beam Frigate - 2(4-5)
Destroyers - 3(as many as you can afford SU wise after the Dread and Tai stuff)
Dreadnought(1) and any captured Taiidani stuff - 4(If done right, you can have 3 Ti HCs by the end of the game)
Repair - 9
Carriers - 8(I always leave my carriers to give the CS a little fire support)