What should we do with https://android.stackexchange.com/questions/12478/is-there-a-gis-application-for-android? The question is equally on-topic for both Android and GIS Stack Exchange.
It's a pity that StackExchange isn't a bit more intelligent with cross-SE site links. I'd say that the questions are related, but there's likely to be a slightly different focus by answerers on each site. I'd have thought an entry in the "Linked Questions" section would be the right way to do it, but not currently possible.
In general it's fine to have overlapping questions, as long as they weren't cross-posted by the same user (without appropriate reason). Linking in a comment is a good idea though.
This isn't generally done on beta sites though (the beta question is closed), although you'd have to ask the SE team for the reasoning there.