Factual error: The coastal wall in Sydney is shown as being inside the Sydney Harbour (right next to the Opera House). But Sydney Harbour is not on the Pacific coast but a part of the Parramatta river, several kilometres from the ocean (where the wall should have been). So the wall is either not shielding the northern part of Australia or (more likely) the producers decided that the audience cannot tell that it is Sydney unless we see the Opera House.
Plot hole: The Kaiju's EMP fries all electrical circuits next to him, and affects the base as well. If that's true, how did the helicopters carrying Gypsy survive the blast without having their electronics fried? EMP pulses induce current in all electronics regardless of whether they're powered on or not. (01:18:00)
Factual error: During the Hong Kong battle, one of the Kaiju disables the Australian Jaeger and the base by emitting an EMP blast. Becket claimed that the Gipsy Danger was immune because it had a nuclear core and was therefore "analog". Being nuclear powered has no bearing on whether a machine is analog or not, and the EMP would certainly affect all the electronic circuitry needed to control the Gipsy.
Factual error: Gipsy Danger's fist bumps into an office table as it screeches to a halt. The Newton's cradle on the table has an impossible reaction. All of the balls would simply sway in parallel, and not the 'classic' reaction displayed in the movie.
Other mistake: In the scene from Mako's memory, the terrified little girl stops crying and smiles when Pentecost emerges from the Jaeger's head/cockpit. But if the Jaegers are 250 feet tall, how could she possibly have seen him? It's not kneeling when she looks up at him.
Continuity mistake: When Gipsy Danger is lifted by the Kaiju in Hong Kong, they end up well above the clouds, and when Gipsy falls she eventually breaks through them. But in the shots when she is falling, you can see that there are no clouds around Hong Kong for miles. That, and Pentecost has a clear view of Gipsy through his binoculars.
Factual error: When the Kaiju "Trespasser" hits San Francisco at the start, F-22 Raptors attack it at the Golden Gate Bridge. The Raptors each fire two machineguns - but the F-22 carries only a single M61A2 cannon.
Plot hole: Gypsy Danger grabs the wounded Kaiju and falls into the interdimensional rift, which opens in response to the presence of Kaiju DNA. That's how Gypsy Danger entered the Kaiju dimension, but Mako and Raleigh somehow escape the Kaiju dimension in their life pods without using Kaiju DNA. Obviously, the rift allows physical objects and energy to pass unobstructed from the Kaiju dimension into our dimension, but not the other way 'round. If this is the case, then Gypsy Danger's thermonuclear detonation in the Kaiju dimension should have burst through the interdimensional rift, as well, at least for a second or so, at roughly the speed of light. Given that Raleigh and Mako had only a 16 to 20 second head start ahead of the blast, they should have been vaporized.
Other mistake: Right after Otachi sprays acid, Gipsy reaches in its mouth to pull its tongue out, but doesn't get affected by any.
Factual error: When the fisherman in the beginning locates the supposed island on the radar he says it's three miles away. The Kaiju (island) then crosses the distance to the boat in about ten seconds. This would mean that the Kaiju swims at a whopping 1080mph (1738 kph) which equates to about Mach 1.4.
Continuity mistake: The crew of Striker shoots Leatherback in the eye, but in the next scene, it's fine.
Continuity mistake: After in the battle for Hongkong Otachi spits acid against Cherno Alpha, the Jäger's head is almost completely eaten away. but when Leatherback emerges and joins the fight, Cherno's head is there again (before it gets ripped off).
Factual error: During the opening scene, the F-22 Raptors battling against Trespasser have the tail code "FF", which is the Air Combat Command's 1st fighter wing based out of Langley AFB, Virginia, while this scene is set in California. The aircraft should be F-15C Eagles of the California Air Guard's 144th Fighter Wing. (00:01:31)