I would definitely question this. If the documentation is present the diagnosis is checked to see if they match up. CMS says the medical necessity is the overarching criteria for a visit level, however it cannot determine the visit level. You can however use the diagnosis to see if the visit level is reasonable for that given medical necessity. For instance if the patient has a skin rash with little to no skin evaluation, then it is suspect for point and click template fill in. If you have skin issues then it is expected that the evaluation will be heavy on the skin and would not includ a GI or GU exam for instance. So the question would be why did the provider consider that a necessary part of this exam or was it simply brought forward from a previous exam.
In addition you could not look at a diagnosis such as chest pain or severe migraine and very little exam and straightforward decision making and decide that the severity of the diagnosis surely warrants at least a level 3 when the documentation is a solid level 2.