i have also had red zebs get dark spots when i changed to a spirulina based food.
recently i had a e yellow go very dark, the same darkish colouring that i have seen people on here confirm as a bad quality fish. she is the offspring of my yellows which are top quality, I put her in a tank by herself & instantly she became the best coloured yellow i have seen. i think it may be due to stress or something, i don't really know what but the moment she was in a tank alone all was normal. maybe yours are not so happy with the conditions, maybe a rearrange of the tank or something might settle them down also