The plot depends on Marcus knowing Khan's people were in the torpedoes and still expecting Kirk to fire them.
Umm, what? Marcus never indicates he would have known. Khan's plan appears to be a complete success: he has smuggled out his crew from a facility controlled by Marcus, with the help of Marcus, without Marcus realizing what the hell happened.
So the torpedoes would not have fired, and nothing wrong with that. Marcus was in the belief that they would fire, would rain death on Klingons, and would ignite a war. He didn't care about whether Khan would live or die; the useful agent had helped with the plan to ignite the war, and if 72 of the 72 torps missed and hit Klingon targets instead, all the better.
(Also, the torpedoes probably would not have exploded, either, so McCoy was never in real danger. Khan would have had no motivation to leave an explosive charge in place in any of the torpedoes!)
How can you do delicate engineering work in that space.
But please remember when exactly Spock learned of the fact that the tubes contained people. He had all the time in the world to do the removing,
before the battle, without telling the audience. And he wouldn't have told the audience, because Khan would then have overheard. That is, there was no plot slot for a scene where Spock would discuss this thing with Kirk, because Kirk was with Khan all the time the camera showed him to us. It's just a sneaky yet extremely logical thing for Spock to have done ASAP when McCoy literally blew the lid on the big secret.
The only reason they have seventy-two torpedoes is that the original episode stated that Khan had seventy-two crewmen
Which makes one wonder whether Khan came up with a completely bogus "rationale" for why Marcus would need to equip the starship of a gullible young officer with exactly 72 torpedo launchers.
Although in fact we don't see anything like 72 (or even 36) holes on the side of the ship. Rather, it seems there are a bit over a dozen holes at most, and each is supposed to allow several torpedoes to "swim" out of the shuttle hangar where they were being stored. What purpose those holes would serve is not known, but it's quite possible they were never intended specifically for the launching of torpedoes, but rather for the delivery of some generic if small auxiliary craft from the hangar.
Timo Saloniemi