A Google Webmaster Help thread has one webmaster who noticed Google indexed his site with the server port in the URL structure. So instead of Google ranking the http://www.domain.com/ it ranks the site, and every page within the site as http://www.domain.com:1234
This webmaster asked if he/she can use the Google URL removal tool to remove these duplicate pages. The only current answer for that is, NO - you cannot. At least, if you do, both http://www.domain.com:1234 and http://www.domain.com will both be removed.
Susan Moskwa from Google replied to the webmaster, explaining:
Are you talking about using the URL removal tool to remove example.com:1234? If so, you shouldn't do that. The URL removal tool removes all versions of a site or URL (www, non-www, http, https, etc.), not just the one you explicitly submit. It should not be used for "canonicalization" -- fixing the problem of having multiple URLs serving the same content.
If you've fixed the problem--especially if you're now redirecting to the correct URL--the issue should resolve itself over time. We also did a recent blog post that you may find helpful.
In general, though, yes it is possible to verify sites with different ports in Webmaster Tools.
So don't use this tool to remove extra ports listed in the URL, to remove a www or non-www version or an https version.
Forum discussion at Google Webmaster Help.