Which of these works to cite when critiquing? I'm citing a study that brings context to my work and some of its methodology is questionable so I am highlighting this aspect. This study was published twice in slightly different forms, once in a lower scale journal with the PhD student as the sole author, and once in a more known journal with both the PhD student and their professor as second author. 

This question partly addresses my problem. At first glance, I would cite the most recent, most prestigious piece. It's shorter but sums the bulk of what I need. However it does not address etiquette. If I cite the study by both authors, the professor's name is joined to the student's questionable methods (IMO). 

Would it be preferable to stick to the work authored by the student only in this case?
It is not your job to protect an advisor from being linked to a paper he chose to sign. Think rather about your reader when making your choice.