Check in your file browser -- maybe you are just "missing something".
Along the lines of what Elie mentioned -- did you rename the files as you imported them? Did you give them an identical name/sequence? If so and like Elie said you opted to not import duplicates, that's likely the problem, and you may need to do an image rescue on the card if you deleted files or reformatted. I always keep importing duplicates on just in case, and I typically name my files with a camera designation when I have more than one camera in a shoot. I may or may not put them in separate folders, depending on the nature of the shoot.