If you want to export to iBooks, you can't use SVG or GIF, and the export will fail if those formats are present. However, even after deleting them from the project, they're still in the Library, and exporting still fails. (Note that if you've ever used a preloader with the provided artwork, you have a GIF in your Library.)
Even if you save the project to a different folder, the images get carried along because they're still listed in the Library. One workaround to delete them from the project completely: save the project to a new folder (to make sure that no other projects using those images will be affected) and then delete the offending images manually from the Finder. You can then export to iBooks.
This may be intended behaviour, but it's a little confusing. I'd suggest that a right-click Delete option would be handy, as would a "Delete unused Library items" menu command somewhere. Or did I miss something?