Steve, there certainly are a number of these photos which have been misidentified, and I have done some studies on a couple of these in the past, resulting, thankfully, in the proper identification of a couple of vessels in photos, which the NHC has accepted as correct. One such is shown at the link below, the USS MACKINAW previously having been identified, incorrectly, as the USS AGAWAM. Unfortunately, some facilities refuse to change their original captions, even though the evidence is overwhelming.
I don't know if there is a master list of these errors, or if anyone is attempting such a compilation, but it certainly would involve many hours of study, and sifting through numerous other resources, etc., to compile such a listing.
Because of my studies on the AGAWAM, I have been able to correct some of these misidentifications. The ten volume set of the PHOTOGRAPHIC HISTORY OF THE CIVIL WAR is notorious for such errors, even showing a view on the USS HUNCHBACK, and incorrectly misidentifying it as the USS AGAWAM. Even two separate views of the same vessel, which, if I remember correctly are on facing pages, are identified as different vessels!!