When the assassin approaches Dr. Quest's ship, he paddles a rubber raft next to it, climbs the anchor chain, and shoots at Dr. Quest. When he is foiled, he dives in the water and swims beneath the surface to just behind a small iceberg. His raft is waiting there for him when it should still be next to the ship.
Jonny, Dr. Quest, Hadji, Race (and Bandit) are locked in the back of a truck. Right after the missile explodes there is a shot of the truck in the background with the doors wide open, and in the succeeding shot the doors are closed again.
The two Baddies who capture Jonny and Hadji individually wear outfits of orange and tan. Orange Baddie has a deep voice while Tan Baddie has a much higher voice. When Hadji escapes and Orange Baddie radios his commander, suddenly he speaks with the high voice of Tan Baddie.
Tan Baddie is guarding Dr. Quest when they take him to the rocket, but when Dr. Quest escapes, his tan outfit becomes orange.
Hadji and Jonny find what Jonny calls "a baby seal," but when its mother takes Jonny and juggles him, it's clear both creatures are sea lions rather than seals. Seals don't have distinguishable necks, can't support themselves on their flippers and are incapable of performing tricks. Incidentally, sea lions are not native to the Arctic.
A real polar bear mother would not be so calm and indifferent when her cub is manhandled by strangers.
There are at least four Baddies out in the open with the Submarine Commander, two with the boys and two guarding Race and Benton. There's only one Baddie with the Submarine Commander when the rocket ship blows up. No explanation is given for what becomes of the other three Baddies (or their submarine) - they're all all suddenly gone.