The Enterprise suffers a mechnical failure of the main coolant system, probably done by the crews bringing the torpedoes aboard, hanging around the engineering section unsupervised. Marcus has her sabotaged while still at Spacedock.
Spoiler: Into Darkness Kirk has a non-Starfleet ship that he gained about a month beforehand during the "Mudd incident". No direct plot/character references beyond that, though.
Spoiler: my thoughts on that Honestly, it's far more likely Marcus had someone sabotage the engines, possibly an agent serving on the ship.