Continuity mistake: Notice the candle on the table in the Italian restaurant scene during Capt. Kirk and Dr. Gillian dialog. It changes height depending who is talking. (01:03:50 - 01:08:30)
Other mistake: When Kirk uses his hand phaser to melt the lock on the door in the hospital operating room, the phaser is not pointed directly at the lock. The beam leaves the phaser at an angle, which is probably not how the phaser would have been designed to operate. (01:25:20)
Continuity mistake: In the operating room, when Kirk uses a phaser to melt the lock, the hand he is holding the phaser in switches hands in the closeup shot. Additionally, the arm holding the weapon in the closeup is no longer in hospital scrubs, but a similarly colored sweatshirt. (01:25:20)
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.