Peter Klein at Organizations and Markets notes a brief dialogue concerning medical research ethics in The Incredible Hulk. Interestingly, the scientist involved suggests not the weighing of autonomy, beneficence, and justice demanded by the Belmont Report, but rather a prioritization of autonomy, allowing the subject, rather than an ethics committee, to decide whether the potential benefits justify the risks. Some ethicists of the 1970s proposed such a prioritization, but the National Commission rejected it.
The only movie I can think of off the top of my head, in which a comparable scene depicts an ethical debate in the social sciences and humanities, is Songcatcher. I haven't seen the movie, but even in the trailer they're arguing about when research becomes exploitation. Maybe I should watch the whole thing.