In his review of Superman Returns for Entertainment Weekly (featured here at CNN.com, Owen Gleiberman describes one of the settings as:
"a crystalline fortress of megalomania, which evokes the remains of the World Trade Center."
I sure hope to hell that wasn't director Bryan Singer's intention. In my opinion, the "crystalline fortress of megalomania" Gleiberman is referring to is suppose to appear as a bastardized version (or bizzaro version if you want to stay within the Superman universe) of Superman's Fortress of Solitude, not a recreation of Ground Zero. Anyone in their right minds and not still suffering from 9/11 shell-shock can see that. Gleiberman is obviously neither.