Oh there are a few I could mention. Like the time that KASE was bugged and it took at least 30 minutes for what had been a very good team with good builds to kill the Scimitar.Though admittedly, I think this was more the game's fault at the time and the battle was truly epic, if mind-numbingly long (I don't know if that Kar'fi driver is reading this, but bless you for playing the bait!).
Then there were some more recent shenanigans. Two in particular involved some idiot and/or griefer blowing the the nanite generators one at a time BEFORE the cube was dealt with on ISE. All the times I've lost CSE because the Kang was destroyed, once before the Raptors came out... .
But the worst, oh the worst... . I don't know if it was malice, stupidity, or mental illness, but this was KASE again. There I am on the right side, alone with my Kamarag, handling the probes. I've taken out one nanite generator in my spare time to expedite things once the left gate was dealt with, since all four of my teammates were over there. Then one of them approaches and starts firing on the second generator. Okay, cool, I've got support now, so I join in. Then the cube warps in and that Kumari that had come to my "aid" bolts. So I'm left alone to deal with the cube AND the probes. Now, I'd say I'm an average to above-average player, but I can't tank a cube and take probe duty at the same time, not without blowing up a lot and letting probes through. So after a few minutes of repeated respawns and about two probes getting through (it was almost four, close, but I got them) I managed to kill the cube. Then Kumari-guy and a Vesta (or was it an Armitage?) blow the transformer, then go after the next two generators on my side and summon the cube, and proceed to ignore it for the go for the second transformer. Deja vu. More probes slip through, but we destroy the gate. MEANWHILE the left has made less progress than little ol' me and the deficient duo, still working on transformer number two (I remind you that through most of the match there were FOUR people on that side). Well, I go over there and help with the probes. I'm a probe kind of guy, I usually load out for crowd-control. Then they blow the transformer, and everyone else concentrates on the gate. So here I am with a swarm of probes to shoot down, being harassed by spheres AND a cube, and everyone else is doing nothing to help directly, mostly just exploding spectacularly against the gate while the cube and spheres take half-hearted pot-shots at them. This was the only time I ever lost Khitomer Accord, and I hope to whatever rules this universe that it's the LAST.