For those of you in the know, it's currently pointless to upgrade the Manufacturing HQ beyond a certain level as there's no need for so many parts. This is going to change in an update coming very soon. High level teams are going to be spending a lot more parts, and there won't be any more excessive accumulation of parts.
In this coming update the Manufacturing HQ will become an essential compoenent to upgrade alongside the Design HQ. If you have a high level Design HQ but a low level Manufacturing HQ, now is the time to begin upgrading Manufacturing. Early in January this update will be coming to link the two HQ facilities.
Put simply: The higher the Design HQ the more parts are going to be required to repair a car. I would recommend bringing Manufacturing up to the same level as Design in the HQ to anticipate this update.