With those who have said it may have hurt them in the selection process, I would be really keen to see the rest of their application. I'm having a hard time figuring out how the dual degree could be a liability. Perhaps they mean that it didn't help them as much as they thought it would (which it won't), but going so far as to say it may have hurt them seems a bit much.
I could see it being a liability in getting interviews for community non-academic positions as they would probably (rightly) feel you were simply using them as a backup in case the big academic centers didn't take you, though this could be dealt with easily by a phone call or two from your letter writers. There may be some stigma that the dual degree kids are lacking in social/clinical skills, but again this would be assuaged by solid clinical grades and good letters. Perhaps in the face of below-average clinical grades, the addition of the dual degree could paint a picture of someone better suited to a lab than taking care of patients? It's a stretch, but that's all I've got!