As the Eagle returns to Alpha, Sandra Benes is clearly seen in Main Mission--she even has a line. Shortly afterwards, the Eagle crashes and she is seen unconscious inside of it.
In Koenig's dream, as he walks down the steps from his office to Main Mission, a studio light is briefly visible in the top right corner of the picture.
In Koenig's dream, his name was spelled incorrectly as "Keonig" in the close up of a monitor screen. It was, however, correct in the wider shots of the same screen.
After the cockpit section of Eagle 1 is detatched, the open door inside still shows the rear rooms of the Eagle's main body.
The door in the cockpit of Eagle 1 bears the number 4, but when Alan goes to open it, the number is now 6.
The "This Episode" section contains several shots that were not present in the actual episode.
The allusion with the title of the "Missing Link" is to the desired link scientists want to find between apes and humans.