I think events around Q'ono'S are where parts of the plan by Marcus (as I think I understand it at least!) potentially give way to some good old fashioned Star Trek style fuzzy logic, because whose plan it all was seems open to debate.
But yes, the ship's engines didn't just conveniently crap out - they were sabotaged because Marcus planned to sacrifice the Enterprise and her crew in order to trick the Klingons into open war. It's to trap the ship (as Khan suggests to Kirk in the brig) whilst he also (I think) eliminates Khan as well. Whether that was by someone who was onboard at the time, or whether it was before they left Earth is not known. They're a silent assassin somewhere.
I think it's partly important to remember that (again per my reading) Kirk's decision to apprehend Harrison/Khan instead of following his orders to execute him without arrest is what fouls up what 'should' have happened. My memory makes me think that Marcus is trying to kill two birds with one stone based on what a variety of characters say and do. However, I've not seen the film enough times to remember everything about the plan that was supposed to have been explained onscreen.
Though I think there are several unanswered questions about said plans even accounting for what's in the film.
Marcus sends the ship in supposedly to carry out something akin to an drone strike on enemy territory to take out a supposed enemy of the Federation, and no-one else would know anything about it. However, he also intends to sabotage the ship and use it as a sacrifice to his plans because he'll get the Klingons to destroy her. But he'll use what seems like the cruel destruction of an innocent stricken Federation ship by Klingons as his excuse for war. Neither Khan nor the Klingons ever know they've been played against the other by Marcus and the only people who might be able to expose him (the Enterprise) will all be dead.
I imagine Marcus knew how the torpedo's worked but didn't know Khan's people were inside (though that for me is one of the fuzzy parts. How did Khan get them all in torpedo's without Marcus knowing? I don't think the answer to that is in the film from memory) them. The only reason Khan even realised the truth is because Sulu sent him the warning message and he would have realised what torpedo's Marcus was using. Which means the torpedo's were not meant to have been used that soon. And the only reason that happened is because Kirk came to the decision that Spock's warning that the Admiral's plan was wrong from an ethical and moral standpoint was correct.
Which makes me ask myself a question about how Khan ended up on Q'ono'S after the attack on Starfleet but I would need to see the film again to see if it's covered by the film anywhere.
'If the Apocalypse starts, beep me!' - Buffy Summers
'The sky's the limit.....' Jean-Luc Picard, 'All Good Things'
courtesy of Saquist