This is confusing to a lot of people. When you downloaded the new version of Numbers the old version remained on your Mac. The new version is in Applications. The old version is in a subfolder within Applications. The icons look similar so it's easy to think you're trying to open a document with the new version whereas in fact the old version has been activated and is trying to open it.
If you tend to open documents from Finder then right-click and Open With ... Numbers.app (3.0).
Or you can open Numbers 3.0 (the one in the Applications folder, not the iWork '09 subfolder) and open the document from there.
Any icons you had on the Dock before the upgrade are of course still pointing to the old version.