The final scene with all of the crypods popping out of the water can come off as unintentionally funny, partly due to the pods breaching like dolphins, and partially due to their bearing a passing resemblance to a British Police Box.
Bower does find himself falling from great heights with a disconcerting consistency. It wouldn't be funny if he was ever seriously hurt, but it ends up resembling a Running Gag, with one such fall being due to a weakened floor panel giving way suddenly as if it were a Trap Door.
When Bower thaws out Commander Payton, he quickly briefs him on what he knows, and tries to jog his memory to get the Commander's help in figuring out what's wrong with the ship. After a few moments of thought, Payton asks with no small degree of irritation for Bower to stop shining his flashlight in Payton's face.