iPhoto has missing photos but they can't be removed
Your Library is corrupted.

Download iPhoto Library Manager and use its rebuild function. (In Library Manager it's the FIle -> Rebuild command) Note: this does not require purchasing Library Manager

This will create an entirely new library. It will then copy (or try to) your photos and all the associated metadata and versions to this new Library, and arrange it as close as it can to what you had in the damaged Library. It does this based on information it finds in the iPhoto sharing mechanism - but that means that things not shared won't be there, so no slideshows, books or calendars, for instance - but it should get all your events, albums and keywords, faces and places back.

Because this process creates an entirely new library and leaves your old one untouched, it is non-destructive, and if you're not happy with the results you can simply return to your old one.