I've already had this problem last year but still have no idea what causes these ugly rusty spots on my chilies' leaves :/ Do you have any suggestions?
My guess is it's a fungal disease, possibly alternaria. I've seen similar things on indoor peppers (as well as other solanaceae plants) with mites. I don't see particular signs of mites, however. Maybe I've seen it on strawberries I started indoors, too.
The main recommendation that comes to mind is to disinfect the area before you plant next year, and the pots, too. Use new soil. Never bring outdoor soil indoors. It can spread diseases and pests that can be hard to eliminate.
Also, mixing a bit of food grade diatomaceous earth with your soil, to keep pests out of it, might help prevent pests from living there and passing on disease, too (if that's the problem). Actually, you could spray water with diatomaceous earth in it on the growing area, and let it dry, to make it more pest-resistant. Any pests that walked on it might eventually die. It wouldn't stop flying pests much, though.
Parasitic algae might cause issues like that. I would avoid clear containers there, to prevent algae from growing, since it grows more with light. Your containers aren't clear; so, I wouldn't think it's the issue.