Plot hole: During the warp-speed chase, the Vengeance literally blasts the Enterprise to pieces, and dozens if not scores of Enterprise crew members are killed and injured in the carnage. The medical crew, including Chief Medical Officer McCoy, should have been working feverishly on the wounded and dying for hours, at least. Instead, as Kirk asks Khan for help, the Sickbay is practically deserted, and McCoy is almost idly conducting blood experiments on a dead tribble. There's no sense of a catastrophic medical emergency whatsoever. It's as though the Sickbay sequence was shot for a different script in which there was no emergency, and then lazily inserted into a rewritten script.
Star Trek Into Darkness (2013)
1 plot hole - chronological order
Directed by: J.J. Abrams
Starring: Benedict Cumberbatch, Simon Pegg, Chris Pine, Karl Urban, Zoe Saldana, Anton Yelchin, Alice Eve, John Cho, Zachary Quinto
Factual error: At one point Khan threatens to target the Enterprise's life support systems which are located behind her "aft nacelle". The Enterprise doesn't have an aft nacelle; as the many exterior shots show, it has a port nacelle and a starboard nacelle. Khan a) is familiar enough with Starfleet ships to know this basic fact about the Enterprise, and b) can see its nacelles for himself on his own viewscreen while he's delivering this line. There is no "nacelle" housing the impulse engines. They are enclosed by the hull of the saucer section. (01:37:25)
Bones: Jim, you just sat that man down at a high-stakes poker game with no cards and told him to bluff. Now, Sulu's a good man, but he's no captain.
James T. Kirk: For the next two hours, he is. And enough with the metaphors, all right? That's an order.
Trivia: As Kirk, Spock, and Uhura head to the shuttle bay for their mission to Kronos to capture Khan, Sulu orders crew to prepare the vessel that was confiscated in the Mudd incident. This is a reference to Harry Mudd, a roguish character who appeared in the original Star Trek series in the episodes titled,"I, Mudd" and "Mudd's Women." Harry Mudd, played by Roger C. Carmel, was the only non-regular character to appear in more than one episode on the original Star Trek series. Carmel was slated to reprise the role in Star Trek: TNG, but he died before the episode could be filmed. (00:44:25)
Question: When The Enterprise reaches Kronos, we see one of Krono's moons was half blown away long before the events of Into Darkness Take Place. In Star Trek VI: The Undiscovered Country, one of Kronos' moons blows half away in an "incident." That incident takes place later on in the lives of the characters when they come close to retirement in the previous reality before it was altered. Are we to assume that either: A different Kronos moon blew long before Star Trek VI in a similar fashion, or that the change of events from the previous film had such a strong butterfly effect that the Kronos moon suffered an incident much sooner than it originally had?
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Chosen answer: The explosion of the Moon Praxis in the original Universe was due to extensive over mining and energy production. In the first movie that took place in the alternate reality, an entire Klingon armada was destroyed by the Narada. It is logical to assume that the Klingons began to over-mine the moon in order to obtain the resources necessary to replace so many lost ships, causing the moon to explode several decades before it happened in the Prime timeline.