When Godzilla leaves the Roman Colosseum, he knocks down and destroys a large section of its outer walls. When Godzilla returns to the Colosseum later, its walls are intact again.
Skar King's eyes are shown to be blue especially in the scene when they show a closeup of his face when he's in his throne room in his introduction, but near the end when he arrives in Rio de Janeiro his eyes are shown to be red or orange.
In the trailer, one of the camel riders around the area where Kong is coming from beneath the ground, begins to run away from the site of Kong's emergence. Shortly thereafter, as it appears it is about to fall into the hole created the camel actually gradually fades out of existence over a couple of seconds. This can be observed in both the trailer, and the final cut of the film available in theaters.
At the beginning of the movie, Kong tries to eat some dead critter but a close-up of one of his incisors shows it to be rotten and it's too painful to chew. In the very next scene, after the lizard steals his meal, you can clearly see that the incisor is no longer rotten in the CGI rendered Kong.
At the start of the movie, Kong is suffering from a bad tooth (canine) on the upper left, shown in a close-up (at about the 4-minute mark) to be decayed, discolored, and the point broken off, requiring an extraction and implant. But, in all the "distant" shots, the tooth looks fine, bright white with a sharp point and no obvious decay, just like the right one.
Kong's left foot briefly becomes transparent when he rides Godzilla.
Trapper assures Dr. Andrews that Kong's new tooth will hold because it's made from the same composite as the heat shields on the vehicles. Heat shielding is notoriously fragile, which is what led to the Columbia space shuttle disaster.
It is clearly implied that Outpost 1 in the outer layer of Hollow Earth was destroyed by an evil ape, possibly Skar King. What appears to be Skar King's eye can be seen in the security recordings. However, not much after the characters discover the outpost's remains, it is said that Skar King and all the other apes have been trapped in the Subterranean Realm below the outer layer of Hollow Earth, since Kong hasn't found them nor showed them the way out. So surely, it is not possible that Skar King destroyed the outpost in the first place.
The humans gasp in awe and terror when they see the remains of outpost 1. 'Did Kong do this?' one of them asks. 'No, it's something much bigger'.
Yet when Kong comes face to face with Skar King not too long after, Kong is slightly bigger than him if anything.
It is established that Kong has been setting traps in Hollow Earth. But when fleeing from the apes in the newly discovered Subterranean Realm, there are several traps waiting for Kong's pursuers. Who set up these traps? Kong immediately began following Suko after arriving in the Subterranean Realm, so he had no time to make new traps.