As noted, capships have issues. Sometimes they don't fire at all - In the end of "Their finest hour", the Sathanas won't open fire on the collusus, making the retail campaign essentially broken.
Oddly though, I've noticed that the vasudan corvette actually does use it's beams on the three freighters in the beginning of that mission, and I don't remember them ever actually firing the beams on them before.
Also, when playing at large resolutions, non native resolutions, the 2-d portion (the main hall, techroom, loadout and briefing screens) are all broken. The actual images are non-scaled and stuck in the upper left hand corner of the screen. Unusued portions leave mouse trails like they're not being updated, though all the controls still require you to click on the spot where it would be if the image were scaled properly.