If you are not happy with a judge's decision, you should take it up with the head official. The head official is usually not the senior judge. In my own organization, the head official was our Grand Master, while the head judges were instructors from various dojangs.
Just take note of the fact that the head official is there to make sure the sport's image isn't tarnished, so you'd better be 100% sure you were treated unfairly before you appeal to him. Because he will make a decision that's best for the organization, which may or may not be in your best interest.
Also remember that you will (unfairly) be labeled a troublemaker, which will disadvantage you in future. Especially in a close fight where the winner isn't obvious.
As always, a personal anecdote: in my very first Taekwondo tournament I faced a guy two years older than me who also happened to belong to the most popular dojang. I managed to beat him in a very hard fight, but the judges decided to award him the win. My instructor appealed the decision to his father (the grandmaster) and I had a rematch. I "won" the rematch too, but for a second time the win was awarded to the other fighter. We appealed a second time. Again I clearly beat him, but the win was again awarded to the other fighter. We decided to leave it as is. Later that day I gave what I felt was a pretty decent performance of Chon Ji (the very first pattern learned in TKD). I somehow managed to score a 5.0 out of 10, even though the lowest anyone had ever scored was 6.5. In fact, the scoring cards only went from 5.0 to 10, which means I only scored a 5.0 because it was literally impossible to score any lower. Clearly I was blackballed.
The only thing that saved me was that my instructor was the head of training for the entire country, so he sorted the guilty parties out afterward. I came back the next year and took 1st place in sparring as well as patterns. I also earned national colours for the first time. The lesson? You run a serious risk of being black balled if you challenge the wrong type of person. Also sometimes life is unfair and the bad guys win.