Using the Structured Data Tool in Google Webmaster Tools I have an error where Google says we are missing the required author, updated fields etc. for an entry that we do not want to have these fields.
Is there a way to tell Google that this is not an Item/Article?
No, there is no way. Google recognizes that you are using it, and either reports that you are not using the Microformat correctly (in which case it’d be a "Microformat error", if there would be such a thing), or that it doesn’t suffice Google’s guidelines for displaying a Rich Snippet (in which case it would be no error, just a notice).
The Microformat hEntry requires entry-title, updated, and author. The Microformat h-entry has no required properties.