There is a rapidly, exponentially, increasing amount of health information. Bias, in various forms, limits the validity of many studies. Once a study is valid, one needs to decide if the results apply to the question at hand. From the wealth of information out there, doctors try to find the valid and applicable knowledge, and then use their judgement to apply that knowledge for the care of individual patients. That's the second half of the problem.
Patients present a great degree of uncertainty.
Everyone is a bit different. Within certain ranges, treatments have different effects. Some patients are more compliant with therapy than others. Lack of compliance can change the effectiveness of therapy, make the condition worse, or have no effect at all. Since diagnosis isn't an exact science, one time when poor compliance with treatment doesn't help is when the diagnosis is wrong.