What is the appropriate course of action for disagreeing with an authority figure? For example... If a senior monk is basing his judgement on personal opinion and not the vinaya, creating dukkha in the community and sowing discord... how would another person (monk or lay) go about addressing this hindrance?
I think it depends on the nature of the opinion and the nature of the disagreement. Sometimes figures in authority positions have to make a judgement call about an issue where the formal rules of the situation don't clearly address the situation at hand. I think that in such a case the person in authority should have their decision respected, provided that the decision is based on the relevant principles to the case at hand and is a reasonable interpretation of the facts and rules.

If their decision is just plain not reasonably based on the facts or the relevant principles then it is clearly wrong and the best thing to do is to decide whether or not it is a big enough deal to want to appeal, and if it is, then one should take the matter up with the next highest competent authority, be it their boss or the HR department.

In the case of a monk the correct response would be to bring it to bring it up with whoever is higher in the hierarchy with respect to the disputed matter. For example, if you have a dispute with the Monk in charge of the lost and found or something in a monastery, the correct response would be to go to the person in charge of the building, or to the Abbot if the matter was important enough.

If it is a very serious matter then one should probably go to the Abbot directly and if that fails, then try to find a senior Monk to get the matter brought to the attention of the local Sangha council if their actions are breaking the Vinaya. And of course it goes without saying that if they are committing serious crimes or putting people in danger, one should contact the authorities as well.

But as I said, authority figures have to make judgement calls when the rules of a situation are unclear and as long as their decision is a reasonable one it is better to simply accept their decision. It doesn't make much sense to fight with an authority figure if it's just a case of "They decided A but I think that B is better."