Plot hole: Yartek tried to disguise himself as Arbitan by wearing Arbitan's robes and pulling the hood over his giant rubber head. Strangely enough, no-one seems to notice that "Arbitan" is now suddenly speaking with a completely different voice, and now has a two-foot-tall-head.
Plot hole: The miniaturized TARDIS crew never interact with the other characters in this story, because, as the Doctor points out, the 'giants' will be unable to hear them, as their voices will be on a different wavelength. So why does the Doctor later suggest using the telephone to try to call for help?
Plot hole: We twice see a map of how far the ice is away from the house, once in the first episode, and later in episode five. The ice has moved most of the way across the map in this time, and the distance it has moved is stated to be a 100 metres. This would place it only 20 metres from the base. The problem with the distance is that it takes Penley quite a while to get the injured Jamie to the base, including a stretch across open ground. Also, The Ice Warriors weapon targeter suggests the base is as much as two kilometres away. So just how far away is the ice; 20 metres, 2 kilometers...or somewhere in between?
Plot hole: When the airlock door is opening at the end of the final episode, the Cyberman is the only one who appears to be affected by the air rushing out. Although 'rushing out' is probably overstating the speed of the 'explosive decompression'. It's not so much an explosion as a gentle breeze...
Plot hole: Just after the Doctor meets the Brigade Leader, he looks at the countdown and says in a very loud voice, "only 3 hours and 22 minutes". Several minutes later, when he leaves the office after stunning Benton, the countdown still reads 3 hours and 22 minutes. Did the countdown clock stop? (00:15:10 - 00:22:10)
Plot hole: The delegate Alpha Centauri is a 'hexapod' - a creature with six legs and feet. ('Hex' = "six", 'pod' = 'foot'.) But throughout this Doctor Who story, Centauri can be seen with all six legs and feet in the air, projecting from the front of the creature... so what is it walking around on?
Plot hole: The Doctor and the Master both surface in bright orange diving suits and are the only two wearing them. But when the supposed body of the Master is dragged out it is also wearing an orange diving suit, and the Doctor and Master are still wearing theirs, so a third suit appeared from nowhere.