The calamity is caused when someone who has died is added to class 3, everyone's memories and records regarding the extra are altered by some unseen force and the extra has a physical body allowing the rest of the class to interact with him/her.
However, when describing what may have caused the calamity to exists, when class 3, 26 years prior refused to accept the girl's death and started to act as if she still existed leading to her being in the graduation photo, it starts off with one student refusing to accept her death and was at first thought to be seeing things until later more students confirmed and the teacher allowed the dead girl to remain in the class.
Did the girl who died 26 years prior obtain a physical existence like how the extra does or did the class just see her ghost?