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In my opinion there's no need to do anything. Nightmare Fuel and Unintentional Uncanny Valley are not mutually exclusive, and in fact the latter can cause the former.
Same with Enjoy the Story, Skip the Game and Play the Game, Skip the Story - you can have both reactions at the same time, nothing is stopping one group of fans to have the former and another group to have the latter reaction.
Yeah the key here is what the audience believes and fragments of the audience can have wildly opposite mileages in terms of what a work has. For example, one fragment of the audience can view a work favorably just as much as another fragment of the audience can view the work unfavorably. We don't disqualify matters because the various parts of the audience had completely different opinions.
YMMV items can only be removed if they are factually wrong or they cause TV Tropes serious problems (edit wars, shipping wars, etc.). If you believe there are YMMV items used incorrectly or a page looks to be blown up in controversy, there are threads on the forums you can consult with other tropers on how to handle potential issues and whether if you need to vet items to make sure the items comply with the YMMV rules and the individual YMMV item rules (ie Broken Base has a 6 month moratorium for example).

I've found two pages with examples that are seemingly contradictory. What should I do about them?