When the Ultra Probe's medical officer looks at the alien ships, the docked Ultra Probe, minus the command module, is visible as part of the group.
Cellini shuts the open docking door (inadvertently trapping the monster inside the ship). When he comes back later, the door is still shut but the monster is now on the other side of the door again (if able to move through a locked door then why wait each time for a docking door to be opened before coming through it and attacking?). (Note: it was demonstrated that the creature possessed the ability to transport itself from one location to another).
Since Helena was obviously American, Cellini should've said "Like Santa Claus, how can you possibly believe", instead of "Father Christmas" (or used his native Babbo Natale).
In referring to Santa Claus, Cellini says to Helena, "...if a man in a red coat and a white beard drove into town, he'd be arrested, certified." It's not against the law to dress up as Santa Claus, so he would neither be arrested nor certified insane.
The script has Helena's opening narration stating that the moon is "drifting between galaxies" when it should have been "solar systems".
During the flashback scene, both Bergman and Dixon point out that the probeship's black box indicates a series of mysterious contacts on the scanner, which may or may not be spaceships. Then Koenig states that the black box recorded a breathable atmosphere "aboard that alien spacecraft."
As Koenig leaves the sick bay, Dr. Russell steps forward from the window. As a result, her shadow is cast and moved across the lunar landscape beyond the window in such a way as to demonstrate that it is merely a two-dimensional piece of painted hardboard.
When the Ultra Probe docks with the "dragon ship", it docks on top of the other one, yet when the crew opens the door, they open the right-side hatch. Then, five years later, when the second Eagle docks with the Ultra Probe, it docks on the craft's right side, yet the crew enters through the Probe's left-side hatch.
During the flashback scenes, a "Space News" update appears on the monitor in the presence of Koenig, Bergman, and Cellini. The news date is Sep 3rd, 1996. The report states that the Ultra Probe launch will take place on June 6th, 1996.
Visible wire pulling monster's tentacles.
In his first encounter with the monster, Cellini attacks it with a hand axe. The axe is in his "lifeboat" when he separates from the rest of the ship, and it still should have traces of the monster's biological material on it, providing evidence to corroborate his story.
Just after Eagle Two docks with the Ultra probeship, Commander Koenig tells Helena to stay aboard the Eagle, but she simply disregards him giving no reason, and follows him and the others off it.