Not enough materials
Why does my factory say "Not enough Materials"?
A factory (or shop) will show as short of materials until it's internal warehouse is completely full. You can set the internal warehouse lower to help spread out a limited supply between multiple buildings, but watch that you don't set them too low and limit your production that way. Also keep an eye on it as your production increases from improving staff.
As a general rule it takes about 2 lower level factories to supply 1 upper level factory, but it's not a perfect 2 to 1 and can vary even more with any upgrades or better staff.
You can try buying what you need from the market to get those messages to go away and increase your production.