I think a lot of the issues people have with “plot holes” in Into Darkness are because Admiral Marcus and Khan were playing cat and mouse with each other from before the movie even started and didn’t have a single consistent plan. There wasn’t a whole Joker-esque “master plan”, the whole movie was the two of them trying to fuck each other over at every turn, and the Enterprise simply trying their damnedest to keep up (and stay alive).
Khan says that Marcus was holding his crew hostage and using them as leverage, so he built special torpedoes to smuggle them onto to the warship he was designing, with the intent of eventually stealing it and ruling the galaxy or whatever (the ship was named Vengeance after all).
Marcus figures this out, and Khan believes that his crew has been killed. He bombs the Section 31 facility as a precursor to assassinate Marcus, but fails. He flees to Klingon space because it is outside of the reach of the Federation, and they wouldn’t be able to bring their full force to bear out of fear of starting a war.
When Marcus finds out where Khan went, he uses it as an opportunity to kill Khan and start a war on his own terms. He sends the Enterprise to kill Khan, giving them torpedoes that had people in them (but clearly still worked as torpedoes because they almost killed Bones and Carol on that planet), and sabotaging the warp drive. The plan was they would kill Khan and destroy the other augments and the evidence of their existence while agitating the Klingons into destroying the sabotaged Enterprise. The Enterprise would serve as a Maine or Lusitania, and start a war that would only further strengthen Marcus’ goals, as well as killing anyone who could implicate Marcus in dealing with Khan.
Kirk’s decision to take Khan alive threw a monkey wrench in these plans, and forced Marcus and Khan to change their strategies on the fly. Khan wasn’t going to surrender to Kirk until he realized that the torpedoes Marcus armed the Enterprise with were the ones with his crew in them because there were 72 of them. He surrendered so that he could come up with a plan to free his people from the Enterprise once he was on board. Khan has escaped captivity on the Enterprise in the Original Series and there’s no reason to doubt he’d be able to do it again one way or another if he needed to.
Marcus only took the Vengeance to meet the Enterprise in the neutral zone after receiving the message that Khan had been taken alive. Once he arrived he was going to manually destroy the Enterprise, kill Khan and the augments, and blame the Klingons anyway, completing his original plan.
The Vengeance almost destroys the Enterprise but they get lucky and have a brief window of safety due to unexpected Sabotage by Scotty. Khan decides at this point that he needs to board the Vengeance and goes with Kirk. As soon as he is aboard he plans to get his crew from the Enterprise and then kill everyone and take the ship for himself.
Spock tricks him and the torpedoes explode aboard his ship, and he decides to crash it into San Fransisco as a fuck you to Star Fleet and then waltz away to come up with a new plan to take over the world, but Spock stops him again and he gets zapped 47 times by Uhura until he can be subdued permanently.
The biggest issue with the story isn’t the lack of logic on the part of the story, its that the entire story is driven by the two antagonists who are fighting each other and using the Enterprise and its crew as little more than tools to assist them in their goals. The only times the crew actually does anything are when Kirk decides to capture Khan instead of kill him, when Scotty disables the Vengeance, and when Spock explodes the torpedoes aboard the Vengeance. Everything else was directly assisting one of the two villains in one way or another.
Also anyone who says that the movie didn’t have a “Star Trek message” must not have been paying attention at the end when Kirk stood at a podium and literally explained the message of the movie to the audience in a speech.