This appears to be a longstanding bug which some folks thought might have been patched back in 2012, but it appears to still be at least an occasional issue, at least on my Linux version.
So, I tried Master Gee for the first time last night and had a freeze/crash right at the point of killing him. The game just stopped, and that virtual desktop was effectively locked up until I manually killed off the Borderlands2 process from the command line.
The exact circumstances of the frozen/crashed death for me was this: I didn’t actually know at the time how to “properly” fight Gee, and while I figured it must have something to do with the post-worm acid fountains, I was never successful that first time in luring him through the centers properly, so the fountains never really went away. The entire ground became filled with the corrosive pool. My character was pretty over-levelled for the fight (had been attempting him on Normal first) so the Corrosive DOT didn’t really threaten me, but Master Gee started taking health damage, while his shield remained at nearly full (I’d been able to bring it down a smidge before giving up on direct attacks).
So basically I just spent quite awhile running around while Gee’s health slowly dropped (but with nearly-full shields). Whenever he’d get near the center of a newish corrosive fountain, the game would beep in time with his DOT health-bar blinking, but that would stop after a bit and not ever beep again (until a new acid fountain was created). Eventually the DOT brought his health down to zero, and that’s when the game froze up on me.
After reading up and checking out a video or two, I was then able to go back in and defeat him “properly” by having him absorb those corrosive fountains, which brought his shield down so that I could damage him properly. Once I did that, I was able to kill him without a freeze/crash. (As an aside, I don’t recall hearing those beeps as he got close to the fountains, when I was doing things properly. It could be that I missed 'em, though.)
So anyway - I’ve only gone through it those two times, but I wonder if in my case it had something to do with that DOT only affecting his health as opposed to shields. On that first playthrough he never ended up dropping his health-regen orb at 25% health, either. I suspect that it just got glitched out somehow near the beginning of the battle, and once the end came the engine just couldn’t deal with it, or something.