The idea that all disagreements arise from ignorance, stupidity, and communications is a point of view that privileges the speaker/thinker, because those concepts cannot always be defined in an objective, repeatable way. So it allows the speaker/thinker to think "I know more, or am smarter, or are a better communicator," rather than "this other person disagrees with me."

Take abortion, for example. Some people believe that human life begins at conception, thus abortion is murder and should be prevented by the government. Others believe that the government should privilege the rights of the mother over the fetus until birth. While these points of view are informed by scientific knowledge, they are not based wholly on scientific knowledge; they are system of human values. So no matter how well we understand the biological systems of procreation, there will likely always be disagreement over abortion.

Or consider people who believe that if they follow the precepts of their particular religion, they will be rewarded supernaturally after death. While there is no scientific knowledge to support that point of view, there's also no scientific knowledge that disproves it either. So if some people think that eating pork is ok, and others think it is a sin, there's not much science (or any other system of objective knowledge) can do to resolve that situation.