The time displayed on the War Clock keeps changing between shots.
(at around 55 mins) After Mako's first drift test, Raleigh goes over to help her as she's coming out of it, there is no suit material covering her neck as she's standing. When Raleigh helps Mako to sit in the Conn-Podd her neck is covered with the suit fabric.
(at around 1h 35 mins) When Marshall is talking with Raleigh about the Mark I Jaegar's radiation affecting him, he turns around from a mirror to wipe his face with a towel. In the next shot, he his significantly farther away from the mirror than he should be, causing him to throw the towel at the mirror.
When Marshall congratulates Raleigh and Mako in the middle of the crowd, he starts walking between them while talking. On the next shot, he passes them a second time.
(at around 44 mins) When Newton is preparing for his first drift with the kaiju brain, he places the headpiece on his head. In the next shot, the collar of the headpiece has fastened around his neck without him touching it.
A Jaeger weights about 2500 tons but it only takes eight CH-47 Chinooks to lift it. A single Chinook can lift about 11.3 tons (11,340 kg = 25,000 lbs).
Throughout the movie, the control team members erroneously refer to enemy targets as "bogeys". A bogey is an unidentified target; once it has been identified as hostile, then it is referred to as a "bandit."
Russian surnames take masculine and feminine forms. So the female pilot Lt. A. Kaidanovsky should really be Lt. A. Kaidanovskaya.
(at around 20 mins) When the Kaiju breaches the sea wall and is threatening Sydney, it is first shown striding under the Harbour Bridge, towards the Opera House. Travelling in this direction, the Kaiju would actually be heading towards the ocean, not coming from it.
By the end of the movie, the nuclear reactor on Gipsy Danger is compared to a nuclear bomb. For starters, reactors are designed not to blow. Nuclear combustible is different from weapons grade fissile material (uranium rods for nuclear power plants are enriched less than 10%; weapons grade enriched uranium is enriched more than 90%).
During the final mission to close the breach, Newt and Gottlieb rush in saying they can only enter the breach with a kaiju since they have some sort of genetic code that grants them passage. Yet when Mako and later Raleigh eject from the Gipsy danger they can pass trough the breach without a kaiju ''code''. The need for the code is never stated as being needed on both sides, especially considering the masters of the kaiju plan on coming through as well.
When carried by the winged monster to the upper atmosphere the pilot says "We are getting out of oxygen". So it implies the robot uses air from atmosphere. But later on the same robot dives underwater without problem. The oxygen is leaking from the damage sustained.
When Dr. Newton and Gottlieb connect their brain with the dead baby Kaiju, The baby Kaiju would not have any memory of going through the "door passage" or any visuals of their world considering it was still in the belly of the mother at that point. However, as stated by Hannibal Chau, the Kaiju are part of a hive-mind network which means they all share the same thoughts and memories.
(at around 23 mins) When the helicopter lands in front of Mako near the beginning of the film, her umbrella is unaffected by the wind.
At various points in the movie in the control room. When members communicate to the Jaeger pilots via the microphone, they do not press the black button on the mic. The Shure gooseneck 515 series microphone requires that the black button is pressed in order to transmit. Therefore, the times characters speak into the mic without pressing the button would result in no voice transmission.
CGI Blood: When Mako points out to Marshall Pentecost that his nose is bleeding, the blood drips from his nose to the top of his shirt collar, despite the collar being under his chin. The blood should have fallen onto his shirt front.
Note that the walking paces of the jaegers do not match the walking paces of the pilots, appearing significantly slower than the pilots' movements, even though the pilots are directly controlling the jaeger movements synchronously.
(at around 1h 8 mins) When Newt is trying to describe the physiology of the Kaiju he likens their two-brain biology to dinosaurs. However, the theory that dinosaurs had two brains was abandoned decades ago.
A Rear Admiral applauding the heroes at the end of the movie is seen wearing the hat of a junior officer. And not only is it the wrong hat, it's way too small.
The scene with the Kaiju breaking through the wall in Sydney makes no sense. Given that the opera house is on the seaward side of the harbour bridge it would have had to be breaking through from the land side of the bridge. If it is already on that side it does not need to break through the wall.
(at around 1h 14 mins) Gipsy Danger is said to be immune to an EMP because it is "nuclear powered" and therefore "analog". This would be nearly impossible as the two have nothing to do with one another. Most nuclear reactors have many digital parts and computers controlling them. Furthermore, the cockpit of Gipsy Danger is filled with what appear to be digital computers.
When the kaiju emits the EMP, it takes out the jagers, the command center, and presumably anything that's digital. But when the Gypsy Dancer attacks, it is carried by a fleet of helicopters, which presumably have the same digital circuits.
When one of the Jaeger is shown to go supersonic, one can see the plume when it goes supersonic. However, the boom isn't a single event. It should keep manifesting itself all along the path of that Jaeger. Further the Jaeger is not aerodynamically designed for supersonic flight so should be damaged more.
During the fights the giant robots run, tumble, fall... sometimes even slide on the ground and capsize. But the pilots keep standing still with minor pushes or balance loss. This is as probable as standing still while a train crashes.
A highly trained operative like Mako should have a better resuscitation technique than hugging and imploring him to come back.
When Gipsy is being carried into the upper atmosphere by the winged kaiju, Raleigh notes that they have no options left. Mako shows him the new sword option, but if they're sharing a thought connection, wouldn't he have known the sword as well?
As the final attack on the breach commences, at 1:46:00, Pentecost informs Chuck that the breach is 3000 meters down. Chuck responds "Half a mile!? I can't see a bloody inch" 3000 meters is close to two miles. It is also odd that someone with an Aussie accent would refer to imperial distances, especially in times of stress.