I have been told the following:
The records at St. Mary's are for the "new" cemetery opened in 1894. Prior to 1894, the cemetery was across the river in Port Jackson. People with relatives buried in Port Jackson were given over 40 years to claim their relatives and re-bury them in the present-day location. Over 1000 bodies were not claimed. So the bodies were moved and buried in a mass grave in Sec 12 with a special marker but no names.
I'm sure folks wanted to move their loved ones but some likely didn't have the wherewithall and others probably procrastinated [after all they had 40 years...] and life intervened.