This is a comparison of images, not just catalogs of sources in images. If you look at the image in the linked article, you can easily spot one of the stars that has "gone missing".
Looking at the brightness of the source that went missing, it is hard to suggest instrumental error - much fainter stars remain detectable in both epochs.
And fraud, really? Who would bother to fake stars in catalogs and plates in the 1950s, and why?