Are the old, with-extension URLs 301 redirecting to the new, extensionless forms? If so, any Duplicate Content issues should be transitory. It simply means that search engines are crawling the new URLs as they discover them, but have not yet learned that all of the old, previously indexed URLs are redirecting to the new URLs.
At least, that's your best-case scenario. And if you're redirecting properly, it's the most likely.
A sitemap is inclusive, not exclusive. That is: It doesn't say "Only these URLs exist, and none others." It only says "These URLs exist, in addition to any others you may happen to know about."