I'm not an auditor for a payer or an authority, so I couldn't tell you how that might play out with one of them, but I'd suspect that the worst case scenario would be legal trouble from the OIG for fraudulent billing. BUT only if fatigue isn't mentioned at all in the medical record. Payers might recoup payment in this situation if they did a post payment audit and discovered that the doctor indicated that the lab was for anemia, and you billed it with the fatigue diagnosis, only because of how the note was worded.
If I were auditing it, I would tell them how it would look if it was coded based on the literal interpretation of the note, and point out that it would cause a denied claim. Then, I might suggest that he simply list the labs ordered in one area, and list the suspected diagnoses and any signs and symptoms that he felt were relevant to his decision making separately, to allow for the auditor/coder to draw the correct inference of which conditions were prompting the diagnostic services. If he is ordering a lab or test that doesn't seem to fit in with the signs/symptoms/or suspected diagnoses, he should then mention what he's looking for with the test, so that the medical necessity is easier to convey.
A good way to look at good documentation is - instead of the doctor making notes solely to satisfy requirements or as a memory aid, make notes as though they're writing them to teach someone else how to practice medicine just like they do. They should give details on what they observed, how they interpreted those observations, and what they decided to do about it, and it should be easy enough to follow for people that haven't gone through 8 years of medical school. That doesn't mean he has to necessarily write more than he has been, but just make connecting the dots a little easier for someone who's not thinking on the same level as an experienced physician. It will come across as flattering, rather than insulting, so they might be more open to your suggestions.