Lot of connectors have this problem, as an example the TE 1-2344715-2.
The female is a shell containing 90 sockets. The male is even without shell, you just insert pins in the PCB in a certain array, leaving the guide and lock mechanism to the housing.
From the schamatics point of view, it is a connector, that have a symbol with 90 connections.
This symbol may also have a footprint that include the 90 holes in correct position.
So far so good.
The problem is in the BOM … where you have a single Jx connector, but actually you should buy 90 pins.
How is it possible to deal with this situation?
One solution could be indicate the connector with footprint, on board but not in BOM, and then add to the schematics 90 symbols representing each pin, with no connections, in BOM and not in board with the correct part number.
This surely works, but for 90 or more pins connectors, maybe with more than one connector per board it looks a little bit clumpsy …
Any other possibility?