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What google (formally known as the machine) is doing is somehow make the determination that the content on the page is suggesting that the page should not be there. And they are doing it correctly.
My position is that a page which says, very nicely, "I'm devastated to have to tell you that we don't currently have any articles about the particular subject you're interested in", surrounded by helpful navigation links, is effectively a very high quality 404 page. But it's not a page that you would want anyone to index or link to or include in the site's page count or do any of the other things you do with pages.
Your statement is plain wrong on so many levels,
As a user, to go to another page to see what you could have told me in place of the link to the empty page is annoying and it pollutes the interweb.
you could just land there via search.