Just randomly exploded, and I'm pretty sure it's X-Wing Alliance Upgrade's fault.
I was doing the Rendezvous with Defector mission, which turned out to be incredibly frustrating. You waste about 7 minutes doing a braindead assault on a space station before following an escaping shuttle back to the Rebel fleet. They get intercepted by a star destroyer and interdictor cruiser, and you have to destroy the interdictor so they can escape.
I failed that like 5 times because I was overwhelmed by enemy fighters and kept getting shot down. Once I finally managed to survive long enough for the interdictor to be destroyed, only for the star destroyer to destroy the Liberty and cause the mission to fail. Each time you have to repeat that 7 minute part at the start of the mission.
After looking the mission up, I was reminded that there's an option to call reinforcements buried in the MFD. Tried that and the mission went much easier. I actually completed it and followed the Liberty to the hyper buoy, where it left. Green on objectives. Victory!
Then... mission failed! The Liberty was destroyed after leaving the system!
I follow the hyper buoy to the next system and see debris floating everywhere. Oddly, there's still an option to enter the Liberty's hangar, and when I try it my X-Wing just explodes.
I'm pretty sure the upgrade patch broke the placement of some ships and the Liberty spawned on top of the Redemption and they both exploded or something. I just skipped the mission after that. Sick of it at this point, and I did win.
Up next is the mission to stop Kupalo from escaping in the shuttle, which is the mission I hated the most as a kid. I only ever beat it once, and ejected from my ship on the way back like an idiot, causing me to fail it anyway.