I think you've got a little misconception there. Parisian bodies in general were not placed in the Catacombs - the extensive tunnel system under Paris actually originates from stone quarries. Most of the early Parisian houses and buildings were built from stone (mostly gypsum and limestone) taken from those quarries.

The reason why it's called the Catacombes is that these tunnels were used to store bodies from some Parisian cemetaries that had become too "crowded" and were starting to become a health hazard. This practice started in the late XVIIth century with bodies taken from the Innocent cemetary and continued until the late XIXth with bodies unearthed during the great public works program undertaken by Haussmann under Napoléon III's orders.

The "official" catacombs (i.e. those that are open to the public) are only a very small fraction of the total tunnel system, most of which doesn't contain bones.

So, to answer your question: mostly, bodies placed in the Catacombs came from too-crowded cemetaries inside the city walls.