In the Silver Age Comics, Brainiac miniaturized the Kryptonian capital city of Kandor. While Superman was able to take the city from Braniac, he was never able to restore it to its original full size. The citizen forever lived in a microscopic city stored inside a bottle, which Superman continually viewed as the one problem he couldn't fix.
In Red Son, they had a similar development with Stalingrad. Superman failed to save it, and placed it in a protective dome. Luthor's note was implying that, in Superman's recent course of action, he had failed the whole of the Earth in the same way he had Stalingrad/Kandor. Superman saw this and realized the error of his ways