Happened to me on Black Talon. Was running a higher level Chiss Operative and I get grouped with a Sith Marauder, Jugg, and Sorc. I should have seen trouble coming right then and there. Now, for some background, I try to play my agent as a sort of blue Michael Weston from Burn Notice, generally making light side choices unless extremely pragmatic to do otherwise, or the victim really deserves it. So we get to the captain and I vote to let him live and win, and all of a sudden I see a flurry of "h0m0" and "smurf" (bloody racists) and "go play for the pubs". I snarked a bit at them and let it slide, just wanting to finish the mission, and make no mistake, I was tearing through the enemies faster than anyone, leaving knives in the backs of everything around me. We get to the general, I vote to take him prisoner, but get outvoted, and right as the mission is about to end THEN they vote me out, not the jerk who "needed" every single drop regardless of whether he could use it, not the guy who jumped on the droids I was CCing, not the one who kept trying to attack the padawan after I told everyone to fall back when they saw her charging up, me.
Took a breath and formed another group to try again, and the two guys, also sith warriors, turned out to be the nicest guys ever. You could tell they were veterans. I'm glad I made that second attempt, 'cause the first one that day was so bad it would have put me off grouping for awhile.
Based on the bolded, I don't think you were votekicked. That flashpoint's bugged. On some rigs the end of the flashpoint boots you to character select. Easy way to figure out if you're one of those is to step into the foundry. Will be booted during the first convo.
Edit: then again, you ran it a second time successfully? Dunno. That's a really, really weird reason to votekick someone and a weird time to do it.