Aside from some of the others noted above, the one bug that got to me was in the final mission, the Ursas did nothing except circle around where they started. As it is really hard to kill the Lucy without Ursa support, while contending with the clouds of Manticores and Dragons it spits out, this may be worth looking into.
EDIT: Just remembered another one. In the mission where you havle to escort all the ships between the three jump nodes (right after the Galatea bites it, IIRC), the ship selection and weapon loadout screens were borked. I could only select two craft of the same type, though it looked like every FS1 fighter and bomber was represented. Also, I could only select secondary weapons, no primaries. Every primary was listed, they just had 0 in inventory. Playing that mission only using Phoenix 5s and Interceptors was an interesting twist, even though I had to use unlimited ammo to pass the mission.