I don't understand the point of the resource factory?

The resource factory lets you claim a bonus amount of resources every 12 hours.This is very useful but you can only claim resources up to the level of your current depot storage cap. If one of your depots is full or nearly full then it will warn you that you will lose any extra resources. This may only be a small amount of a resource you don't need much.

To avoid losing any resources you can use up your current stock with upgrades / evolution etc. Or you can upgrade the depot buildings to increase the cap.