You are failing to differentiate the semantics between cemeteries and mass-graves. Cemeteries contain the bodies of those that have died over an extended period of time, typically decades or centuries. Mass-graves contain the bodies of those that died over a short period of time, typically plague, massacres, or genocide.

The Paris catacombs are actually cemeteries that overflowed their surface square footage. By the late 1700s Paris had grown to a size that the local church graveyards could not contain the dead. To make room, the bones of the long dead were excavated and placed in an ossuary to make room for the newly dead.

As ossuary sites in Paris ran dry in the 18th century, bones were relocated to the abandoned limestone mines beneath Paris, leading to the catacombs we now know.