These are about ~6 extra minutes in the longer version. Is this a single portion that was removed or several? Why is this difference present in these two versions of the movie?
According to Imdb's Carnival of Souls Alternate Versions page:
There are at least three different versions to be found on video/Digital Video Disk. First is the 84 minute director's cut which includes an extended conversation in the organ factory, a scene between Mary and a gas station attendant shortly after her first seeing the man,an extension of the scene where Mary first goes to the church, an extended dream/otherworld scene, and a scene between the landlady and the doctor shortly before Mary leaves to go back home. This is the version that Herk Harvey premiered in Lawrence Kansas in 1962. The 81 minute version contains all of these scenes, except the extended scene in the organ factory, and a few short shots. This is the version that Herts-Lion released in 1962. Then there is the 75 minute version which contains none of the extended scenes or other additional scenes.
The page also notes that the films 1962 distributors cut four minutes from the film but doesn't cite a reason.