Revealing mistake: When the whales first swim past the now submerged Klingon Bird of Prey, if you look to the right where the water is supposed to meet the distant horizon, you can see an exposed edge to the 'horizon' as the water moves up and down. This is the edge of the pool they are in, and the exposed edge is the bottom of the painting of the sky behind them. (01:46:30)
Visible crew/equipment: During the scene on the bus, two members of the camera crew are visible in the window behind and to the right of Spock. The crewman of the left is sitting and operating the movie camera, and the crewman on the right is taking still camera shots. (00:43:50)
Visible crew/equipment: During a close up of the police officer's sunglasses, when Chekhov is asking for directions to Alameda, some crew are visible in the left lens. They are a line of people trying to stay out of the camera. (00:43:30)
Continuity mistake: In the scene where Spock gets confronted after swimming with the whales: you can easily see before he puts on a robe, that his clothes are completely dry, yet he had just been swimming in the shot a moment earlier.
Visible crew/equipment: At approximately 01:32:50 on the Blu-Ray, you can see a diver releasing the mechanical whales. He is on the far right side of the screen, you can make out his head, body and left hand. He is visible for a good 8-9 seconds. If you have a different media source, it's during the Bird of Prey decent. You see a closeup of Kirk, followed by a closeup of Uhura and Gillian, then a close up looking down on the harpoon. It's in the following scene. (01:32:50)
Continuity mistake: In the scene with Kirk and Spock walking the marina green under the Golden Gate Bridge, the leading shot shows blue sky. As the camera changes angles, the background changes to completely fogged in. Not shot on the same day.
Factual error: When the Bounty is preparing to slingshot around the sun, the sun is burning a light yellow. From space, it would be white; it only appears yellow when viewed from Earth because of how the visible color spectrum is filtered through the atmosphere.
Audio problem: When Gilliam slams on the brakes, the tires make a screeching sound, but the wheels come rolling to a stop, ergo do not skid. (00:56:50)
Plot hole: If the Bird-of-Prey went to warp speed right after the whales were beamed up the ship would have already been so far away from Earth it would have been on its way back towards the sun, yet minutes later the ship is shown leaving the Earth, still at warp speed.
Continuity mistake: When we first see the whale pen it is divided from the sea by a concert wall with double gate in the middle, but when the whales are released most of the wall and gates are missing.
Revealing mistake: When Kirk and crew flee the hospital McCoy bumps a man with his leg in a plaster cast. Look closely at the cast - it is fitted over his PJ's leg like a boot, plaster casts are never fitted over clothing.
Factual error: As they descend into the park, Uhura gives a bearing and range of 283 degrees, 15.2 kilometers to the whales, which are supposedly in a marine park in Sausalito. 283 degrees would put you in the Pacific Ocean, because Sausalito bears around 360 degrees from the park. Uhura gives a true bearing to the whales, since a relative bearing would be useless once the crew leaves the park.
Chosen answer: This question has been answered a number of times by various individuals, all saying pretty much the same thing. The answers have been most satisfactory given the question revolves around a fictitious situation and the answer (s) need to be accepted as complete for this purpose. Any dispute or non-acceptance should be addressed in a Star Trek forum. Any ignoring of the Prime Directive was done to save the future of Earth, as the probe would have wiped out all life on Earth. Essentially, nothing that was done in the past resulted in major changes that would make Earth 300 years later appear any different, and no major futuristic technologies were revealed. The major one, Chekov's communicator and phaser being left behind did not result in anybody learning secrets. In the film, the phaser didn't function because of the radiation. It's presumed then the radiation permanently damaged the equipment so it appeared to be nothing but a toy or prop. However, in the novel "The Eugenics Wars: The Rise and Fall of Khan Noonien Singh", Roberta Lincoln was sent by Gary Seven to recover the items from Area 51 before any secrets were learned (and as stated before, additional corrections to Earth's timeline could have been done that aren't addressed in the film.) The subsequent loss of a suspicious "ruskie" would have hardly affected the era that was already in the midst of the Cold War. McCoy even questions that giving Dr. Nichols the formula for transparent aluminum could alter history to which Scotty replies what if Dr. Nichols is the one who invents it, to which McCoy agrees (in a later novel it is reveled that Scotty already knew Dr. Nichols invented transparent aluminum, so history was not changed.) The miraculous recovery of the old lady (growing a new kidney) was done by a pill so that any examination of her would not reveal the futuristic method involved. She would be a bewilderment to the medical community at best, and most likely misdiagnosis would be to blame. And just because she got a new kidney does not mean her life would have been extended, she could have died some other way in both timelines. And as stated before, Gillian simply wasn't vital to Earth's history. She could have contributed nothing of importance to society and died alone and childless. And a missing pair of breeding Humpbacks would hardly affect the extinction of their species, however in the future, they are already extinct, so little changes would occur. As for any questions about people seeing the Klingon ship in the past, who would believe them? People have long been claiming to see spaceships and aliens to little or no avail, so why would anyone believe a handful of people who said they saw aliens in a spaceship steal 2 whales? However, as with many time travel situations in films and novels, it's possible the events of the 23rd century as they appear in the beginning of the film are a result of Kirk and company's actions in the 20th century since the events already occurred even though Kirk and company had not yet done it themselves (this is where a discussion forum on the film would be advised, or a discussion forum on the theories of time travel).
Possibly the most convoluted and poorly-reasoned series of answers I've seen on this site. So far.
Charles Austin Miller
I think they're pretty logical actually.
I think your opinion would be in the minority. There is nothing exceptionally convoluted, nor poorly reasoned in the response.