I think, to be honest, people just get very confused by the whole Doctor Who tag structure on AO3 - what I call 'kitchen sink' tagging is common across the archive, and it's basically people who don't know how to tag. So polite comments might get you somewhere, although some people don't take kindly to anything that's not related to their fic, understandably.

There used to be a lot of how to tag posts going around but everyone's given up.

(The other thing people do is just to tag with 'Doctor Who' which is even worse, because then it doesn't show up in anything beneath the meta-tag, & if people are, say, following a Classic Who feed here, then they won't see the work at all.)