I don't think it's questioning anyone's competence to suggest that a single scientific result might have confounding factors. This is one study done by one team. If the result was repeated in several studies, all coming at it with different viewpoints then I'd start to believe the result. In this particular case though, there seems to be new research coming out every few months saying coffee is good or bad for you. If the results look like that then it's hard to put much weight on any single one of them.