When Admiral Nelson and Captain Crane are interviewing Chief Sharkey in the Admiral's cabin, in the wide shots of the three the Admiral has his four stars on his collar, but in his close up they are missing. Also later when Nelson and Crane are watching the video of the murder, he is also missing his stars on his collar.
During fight in Flying Sub Captain Crane's stunt double is much heavier than David Hedison.
The imposter somehow knows how to operate the flying sub, this is never explained.
At the end everybody is relieved about catching the killer and completely oblivious about the Moon which is presumably still heading toward the Earth.