Pages being created automatically with different permalink structure

We created a blog back in 2008 which was our first one and since it has grown into a very large sub site of the main domain. It has always ranked very well on Google along side the main static site.

Just recently we have seen rankings dropping and investigating on Google Webmaster Tools it seems that Google has somehow crawled some phantom pages on the blog and links from them to other phantom pages are returning 404 errors.

The Permalinks structure was set to custom using – /index.php/%postname%/ – This is not how we would do it now but this blog is our oldest one.

It definitely seems that the blog/database is somehow creating its own pages & categories based on the actual ones we have created but using the default WP structure, although these pages/posts do not show in the WP admin interface.

Examples:

Actual blog posting = domain.com/blog/index.php/hello-world/

Phantom posting = domain.com/blog/index.php/page/19/

Because Google has now crawled these mysterious pages/categories and they are producing errors by the bucketful traffic to the correct pages of the blog has almost vanished but as I don’t know where these erroneous pages are being stored or how Google initially found them I really don’t know what to do about telling Google to ignore them.

The blog is very big so I really want to get it resolved, so any suggestions are warmly welcomed!