FamilySearch, Ancestry.com, and other sites create their own indexes to certain records. There may also be "older" or "original" indexes to these same records. The National Archives created many card indexes to certain records, particularly in 1930s and 1940s. FamilySearch has digitized some of these card indexes and put them on their website.
Passenger lists for Philadelphia are an excellent case in point where there are "new" indexes and "old" card ones: