Resources Won't Increase
There is a limit^* to how much raw materials your outpost can safely store. You can increase this limit by repairing and then extending the Biospheres (for food) and the Storage Facility (for erythium, gas and energy).

* To find out about your current Storage Limits, hold the mouse cursor
over the resource icons at the top: , , and .

To repair the Biospheres, you needed to extend the E.D.E.N. Farms to level 2, which you already did. Now, to rebuild the Storage Facility, you will need to raise all 6 Erythium Mines and all 6 Argon Extractors to level 2. Once resources cannot be stored due to lack of space, all production is converted to BC (at a rate of 4 resources for 1 BC).

I have repaired those storage facilities

I didn't quite got that food thing...