Not sure if this really qualifies as a "bug" or just me sucking as per usual, but in that mission where you jump into Phi Eridani to secure the jump node (the mission is named Swimming With Sharks, and you must protect the GVCv Andrasta), and you get jumped by a couple Shivan capships; to wit, the SC Nightgaun (Rakshasa), the Tulzscha [sic] (Lilith), and then the SCv Tsathoggua.
Often I've found that if the Tsathoggua has not taken enough damage by the time the relief fleet jumps in (GTD Valhalla, GTC Andronica, GVCv Nefertem), they will simply continue to their designated waypoints, completely ignore the Tsathoggua once out of beam range, and then the mission is unwinnable, as you cannot kill the Tsathoggua (no bombers, you're flying Herc IIs).
Only way I've found around this is to order almost everyone to attack the Tsathoggua, ignore the Tulzscha (it's supposed to run away, but I distinctly recall killing it the first few times), and keep just enough bombers off of the Andrasta to keep it above about 30% hull integrity; which seems counterintuitive; for example, my initial idea was to intercept bombers, disable the beams on the Tsathoggua, and then disarm/destroy the Tulzscha as soon as it jumps in (since it's the biggest threat to the Andrasta with its LRed, and being a cruiser can be taken out by Herc IIs), thus leaving the crippled Tsathoggua for the allied capital ships to mercilessly blow away.
However they simply ignore it. I tried speeding up the mission to see if they would turn around and finish it off, but they instead sit placidly at their waypoints and nothing happens.
Basically the only way I've found to really finish the mission is to pound the Tsathoggua as hard as possible for as long as possible (that's what she said?), while doing the bare minimum to ensure the Andrasta survives, and even then most of the time the final damage is done by the Valhalla's green blob turrets since the beams are already out of range/not firing for whatever bizarre reason.
Everything else works fine though ^^