On my last steam import, several items did not get imported so I added them to the new request section (the new C&C collection, newest Humble Choice stuff, and a couple misc). After a day, a few of them were marked as already on the site and so I hit import again, and they popped up. Today, a few more were marked as already on the site so I deleted the requests, but when I import they still aren't being found.

Is there a separate place to report games that are on the site but not importing properly from steam?

Unfortunately, item requests and the Steam import are independent queues and aren't always worked in tandem. I try to handle them together when I spot requests that maybe came through via Steam, but I'm sure I miss some from time to time and I can't speak for others on how they handle it.