When Gloria Guida (Michelle) is having her legs crushed during the dive on the ruins of Atlantis, a first sequence shows Guida with both legs trapped under a single pillar. When the diving team comes to her rescues, she is then trapped under a pile of rumbles and the sea floor scenery is different.
When the survivors come in to let Michelle know her parents were washed overboard, Peter walks in empty handed. When he leaves the room, he has a drink in his hand.
When the divers enter the water (38:30 - 39:20) they are all wearing buoyancy vests. Once they are under the surface, the vests are gone.
The US military planes are flying at different, varying speeds and are constantly changing formation, contrary to their earlier instruction to fly in standard formation.
When Michele is taken on a life raft to Bimini, it is around sundown. The next several shots are either in the dark or sunlight.
In the fourth minute, Ft. Lauderdale (air traffic) control tower has no name or designation on it.
In the 75th minute with the ship listing in a storm, mother and daughter are on their bed which tips to one side. But the picture hanging above the headboard tips in the opposite direction.
When the aircraft pilot in the Bermuda Triangle declares he doesn't know which direction he is going, the sun is a constant compass. Even if he didn't know exactly where he was, the sun would guide him westward to land.
The U.S. Navy officers seen onscreen are wearing uniforms are very obviously not U.S. Navy uniforms.
The reenactment of Flight 19 shows only four planes, while the actual training mission consisted of five.
Around the 50th minute something causes the underwater pillars to collapse. If this was an earthquake, the pillars would not have continued collapsing for so long, nor would a result be what appears to be sea foam atop the ocean.