I notice you use relative addressing on your pages. This is not good, since one single mistake can "create" phantom directories or many pages in a directory that doesn't really exist.
Your initial problem was probably caused by a relative link to "catalog/Some-Page.html" (no leading "/") on a page that was already in the /catalog/ directory. This would have automatically created a link forward into a /catalog/catalog/ folder (as Google followed the link), and any relative links on those pages would also look like they were in /catalog/catalog/.
If it's not possible to use a fully-qualified link (that includes the domain name), at least create a link that is relative to the root directory; that is, with a leading "/" character. E.g.: href="/catalog/DIY-Supplies-p-1-c-251.html"