Superman saw the blood because you don't need microscopic vision to see blood on a guy's face. He just didn't jump to the conclusion that the blood meant that Zod is an unrepentant psycho killer.
No one had ever escaped from one of Superman's containers before. He had no reason to believe that they weren't inescapable.....until Zod escaped from them. They'd always done the job before. He'd never had reason to doubt their effectiveness. He had no reason to believe he was putting anyone at risk.
He doesn't seem naïve or dumb. He seemed like a guy who wasn't omniscient.