The premise for the episode is that everyone in in the world, apart from the crew of the Seaview, has vanished. Yet the view from the window of the Flying Sub flying over the Virginia coastline shows cars and trucks driving down a road.
When the "flying sub" is on the surface of the ocean near New York, it is rocking rather violently. Yet inside the "flying sub" all is motionless.
38:30 When Captain Craine is summoned to Sick Bay while talking to Chip about the X-4 Chip responds "Aye-Aye" but his lips don't move.
When Adm. Nelson asks Sen. Dennis to pick a submarine, he points to one near Hawaii. Nelson states its coordinates are 21° 59' N, 160° W. He then orders Sparks to contact the sub to verify its location. When Sparks calls back he states its coordinates are 41° 59' N, 160° W, to which Nelson and Dennis agree was a perfect match. The coordinates Nelson gave is the correct one for Hawaii and the one Sparks reported was much further north.