When they carry the two nukes to the plane, they put the second one under it just when the team has walked on board. When the president comes, they once again carry both nukes to the plane.
After the fire in the tunnel, the girl gets out of the trunk and touches the car many times. She shouldn't be able to do that without getting burned.
Blackberry handheld units do not operate on the wireless network out of the box without activation first.
When the two helicopters check for the status of the team in the supposedly evacuated and empty Los Angeles, normal commuter traffic can be seen crossing a bridge.
Early in the film they say the telephones are not working but later in the film you hear a telephone beeping.
Dr. Sallin describes the need for a 15 megaton device, 100 times the size of the Hiroshima bomb. 15 megatons would be 1,000 times the size of that bomb.