Or at least so Marcus claims, after Kirk reveals this fact to him in their discussion. Perhaps he just doesn't want to look stupid? It wouldn't make much sense for Marcus to knowingly let Khan smuggle his crew out in Kirk's ship. Marcus only controls Khan through these prisoners - why should he give up that advantage and donate the prisoners back to Khan for no gain? Timo Saloniemi
Khan hid his crew in the torpedoes. Marcus found out. Khan fled and caused hell. Marcus went into damage control mode. He let the Enterprise have the torpedoes. He knew that they were the perfect tools to stop Khan, either way. And he could then, as he did, blame everything on Kirk and his crew, helping Khan and his crew to escape. It's a very convoluted way to shift the blame away from him, stop and kill Khan and still get his war with the Klingons and styling himself as the hero of the first hour.