When Jonny levitates up and down, his socks are white (or his sneakers are high-tops), but while he's up in the air his socks are blue (and his sneakers are definitely low-tops).
When Dr. Quest and Hadji leave for the mainland, there is no portable communicator dangling from Jonny's belt; yet, in a moment, Hadji calls him and suddenly Jonny is wearing it. When grabbed by Svedri, the communication is once again gone, yet when Jonny's tied to a ladder, it hangs from his belt again.
In compass reading, there are 360 degrees, with north being 0º and subsequent degrees numbered clockwise. When Jonny relays the travel direction of the Prober to Dr. Quest, the arrow above the controls alters between 5º and 6º (slightly east of north), but Jonny says 325º (which is 10º north of north-west) and bearing "117" (slightly south of east-south-east), yet Dr. Quest concludes they're heading south-south-east (which, to be precise, would be 157.5º).
Race exits the Prober through its side door. Since there's no air chamber between the door and the Prober interior, and since no large volume of air belches out into the ocean as he exits, it would mean the interior has already been fully flooded (with others in the Quest party drowning inside). When Race reenters, Jonny, Hadji, Bandit and Dr, Quest are not drowned, nor are they even wet.
Race dislodges the metal time bomb from the exterior of the Prober. It immediately floats upward because, apparently, metallic bombs packed with explosives are far lighter than water.