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I use php includes so links in those go from the root like "/abc/xyz/blah.php" so if the bot is on a page in a directory called "/jql/blah2.php" and it has a link to the above page, it's trying to go to "/jql/abc/xyz/blah.php" which it's never done before.
All I've done is make a php script that inserts different meta descriptions based on the page name and add a google nosnippet meta tag.
Why might it be doing this?
It should stop trying to index the pages when it gets a 404 error for them?