Yeah, the missiles were the oddest part of the story (which is bad considering they were also crucial).
At first, I thought maybe Marcus was giving Kirk the missiles having put Khan's people in them as a way of getting rid of them after Khan went rogue. But that's too convoluted to make any sense at all. Especially taking care to put them in still frozen and alive.
It turns out, anyway that Khan put them there, himself. So maybe it was a way of getting them onto the Vengeance, where those missiles were probably intended to go in the first place. Seventy-two Trojan horses. Once they were there, Khan would find a way to board the sparesly crewed ship before the missiles were fired and revive his friends (if Scotty could run around the ship undetected, Khan certainly could get aboard and find a way to revive his people). Khan and his people would then take control of the Vengeance. That meddling Kirk getting the missiles was not what Khan believed would happen. There are problems with this premise, too, but it makes some sense.
The final problem is there are exactly 72 missiles. What a convenient number. Wouldn't that raise eyebrows among Marcus's people? Did they coincidentally order 72? What if the initial order was for only 64 missiles? What if there were 84? What if only 50 had been loaded onto the Enterprise?
I like this explanation.
Although Marcus did not seem to be surprised that Khan's people were in the torpedoes. Maybe he's just a great manipulator.
Plus, they had to redesign the Enterprise [somehow, somewhen] to give her 72 launch tubes. She didn't have those in the last movie. How convenient that Enterprise has exactly 72 launch tubes.
Does the Enterprise have 72 launch tubes. they could use the same launchers again as they did in the series.