I had this same problem but when I accessed the photos through the camera, the black boxes were gone and the deleted pics were removed as well. I think it is a bug that appears when you delete multiple photos from directly within the camera roll. It should go away after a restart or on it's own.
this has happened to me on my iPhone 4 a few times. it usually happens right after syncing with my computer, and usually exiting the photo app then waiting a few minutes, then going back in fixes it. or restarting the phone as a few have said.