I think it is not so much that the medical system has been telling us the lies, as that they were also deceived by the proclamations issued by the large manufacturing companies, defending their products.
Crisco started out as a grease for machinery, when the proper petroleum-based grease was not available, due to the use of it during the war. So, they figured out how to hydrogenate vegetable oil into what we now call shortening, and they used that for mechanical grease.
After the war, there were whole plants set up to process the vegetable oil, so they tried using it for cooking, renamed it "Crisco", and told the world that it was much healthier than butter, since it was made from pure vegetable oil.
Just one example of where big business has influenced the medical profession to back up their story, and help sell the product. Some probably knew the truth; but since most modern doctors actually study very little about nutrition, most of them probably just followed along with popular opinion.