I have trouble following.
Did you only send a faculty letter when they requested a professional LOR?
Did you not even send any letter to the medical school (it was sent to some other program)?
Did you do both?
Did you use AMCAS to submit letters?
Was this an additional letter sent after an interview? If so, did they specifically ask for another letter. If they asked you specifically for this, then yes, it will look bad.
If you were given an interview based on letters initially sent, then you should not be worried.
If you wanted to add another letter (but the school did not request one), then how would they know if they never received it? You can always resubmit it.
Note: I am just an applicant and can not tell you what ADCOMs think. You can always contact admissions.