What should you do if a co-author has an unethical affiliation? A person I know was in the process of publishing her first manuscript when her supervisor told her to add his newly acquired affiliation from a university in Saudi Arabia to his name. The Saudi Arabian university hired this Supervisor as guest faculty and were essentially paying him for adding them as one of the affiliated universities in all the forthcoming manuscripts.

This was of major ethical concern to my acquaintance.  In recent years, Saudi universities have been accused in multiple different prominent articles of "buying rankings" by paying prominent faculty to list them as an affiliation, even though the faculty have little real interaction with the university.  To many, this looks like simple bribery or unethical sale of reputation, particularly give the high sums of money involved.

My acquaintance was concerned that, if her advisor was listing this affiliation on her paper, then she would be aiding and abetting in this unethical behavior.  Unfortunately, her confrontation with her advisor went badly, and although she was able to publish the paper without the questionable affiliation, the relationship was destroyed and she ended up resigning the laboratory under pressure.

Now my question is this: what should a junior researcher do when they feel they are being asked to be party to "affiliation fraud" of this sort?  We would not ask a person to remain silent if they thought a co-author was being unethically added or removed.  Should unethical addition or removal of an affiliation be treated the same way?
To my mind, this case is very similar to the question of whether somebody can essentially pay for co-authorship.  We see many questions of this sort on this site, a particular apropos example of which is this one, which asks in part:


  Suppose I'm a billionaire who knows nothing about science, but I take it into my head that I want to be (regarded as) a famous scientist.


The case of the Saudi Arabian affiliations looks to me very much like a parallel construct:


  Suppose I'm a billionaire institution which does little significant research, but I take it into my head that I want to be (regarded as) a famous institution.


I think that it is completely reasonable to find this problematic, and to object to a co-author adding this institution, just as one might object to a co-author adding the billionaire know-nothing as another author.

Now the question is what to do about it, and, as in these authorship questions, the advice tends to depend strongly on the power dynamics of the situation.  On this site, we often advise students to leave bad situations rather than creating a confrontation, due to the power imbalance with faculty.  For people in positions of power, however, like tenured faculty, it is an effective endorsement of unethical behavior if you are aware of it and do not call it out.  It may not be a hill to die on, but either you care enough to make your voice heard or else you accept the behavior as legitimate.  

In this particular case, the student may have acted unwisely with regards to safeguarding their own future, but it may also have been important enough to them to take that ethical stand.  It's impossible for us to know how important it was to that person, and it's easy to engage in post-facto critique of their tactics, but I think the concern is legitimate and the actions taken are within the range of reasonable options, depending on how strongly the student felt about the ethics involved.

In short: some people choose not to take military money, not to work on espionage-related research, or not to publish in non-open journals.  Choosing not to be party to what you perceive as bribery for prestige is just as legitimate an ethical choice to make.