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?