Need to see a screen shot of what you are seeing both in the Import window and the Library module.
Have you done a search in LR Classic for the File Name of one of those images using the Filter Bar Text option and having All Photographs selected in the Catalog section of the left hand side panel?
In my experience LR does not make such errors. But I gues anything is possible. Without doing a thorough search for the file name or names of one/some of those images that you think are not in the catalog you really don't know.