I don’t know what people think you learn in medical school that makes you an infallible source of health knowledge.
The problem is not with evidence-based medicine itself, but with how the evidence is generated. The gold standard of medical evidence--a large, randomized, double-blind clinical trial--is extraordinarily expensive. In practice, much of this research is funded by private industry, which must have a reasonable expectation of earning a return on its investment. That naturally directs research toward treatments that can be patented, commercialized, and sold at a profit.
This creates a structural blind spot. Many naturally occurring compounds cannot be patented in their natural form, making it difficult to justify the enormous cost of conducting the kind of trials that modern medicine demands. As a result, potentially useful natural therapies often remain under-studied, not because they have been proven ineffective, but because the economic incentives to investigate them are weak.
This is the reason your doctor is much more likely prescribe Ambien CR than to suggest trying magnesium supplements.
Do you know they’re wrong? Please don’t invoke Dunning Kruger like this, it’s cliché and also wrong to do. There’s no indicator for whatever it is Dunning & Kruger showed, you cannot know if it applies to a single person. Their main plot showed a positive correlation between confidence and competence. Their paper has problems, their methodology has been rightly questioned, and some attempts to reproduce have failed. Plus keep in mind that, ironically, for people who are intimately familiar with the debate over DK, using it to essentially name-call someone backfires and has the opposite of the intended effect, it makes the name caller look confidently ignorant.