I'm a little confused so I'll give advice on 2 possibilities:
1) If the physical exam literally states "The exam was completely normal" or "A comprehensive exam was within normal limits" that is not sufficient documentation to get credit for a comprehensive exam. You are allowed to list negative findings, but you can't just say the whole thing was normal.
2) If the patient is seen for shortness of breath - but the physical exam documented is a template and seems to contradict that by saying that the respiratory system was normal, lungs clear to ausculatation with no wheezing - then one of two things is happening. Either the physician's objective findings truly do contradict the patient's subjective complaints (somewhat common, especially in the ER where people might be overreacting or even attempt drug-seeking behavior.) OR - and this is the one I'd be more concerned about - the provider is using a templated note and not sufficiently editing it to make sure the findings are correct.
If I were in your shoes I would count it for the note you're looking at, but meet with the provider, review your concerns, and make sure they are aware that overuse or abuse of EMR templated exams and "cloned notes" are one of the hot topics that the Office of Inspector General have identified on their Work Plan, and they are focusing on notes with identical exams - especially if the findings are medically impossible or improbable.
Ultimately the medical necessity should support the extent of the history and exam documented, but with today's EMRs it can become tempting to adopt a 'point-and-click' mentality where the provider might just click until the documentation meets the level they had in mind, rather than the other way around.