It can't mean version history, or else FindUrlById wouldn't work ( https://gist.github.com/601848 ) - it specifically expects one url, and opens the SPItem to find the version Url.
I have an issue with two documents with the same Document-ID (docx file and a pptx file), and not sure it's related. The default document-id is link also misbehaving.
Under what circumstances can FindUrlsById return more than a single item?