This has been why we don't use github's issues, wikis, and why we won't use their projects. For example if the overall product has a web site repo, server repo, iOS repo and an Android repo then they need to be used as a coherent whole. An issue might be reported against iOS but the cause is in the server, so the ticket would need to be moved. Rinse and repeat for all the other interactions of piece, and that collaborators often don't know (and shouldn't need to) precisely what issues, wikis etc correspond to which repo.

The now defunct Google Code had a very good solution for this. You could create additional "sub" repositories alongside the "main" one. Github already does that for the wiki, but doesn't generalise it to allowing additional ones. I'm somewhat convinced this is because github has the whole "charge by the repository" model, which is at odds for being useful for projects that require multiple git level repos.