Plot hole: One sequence which makes little sense is when Ace triggers the booby-trap gas grenade on the chess board. Although the Doctor places a wastepaper basket over the grenade, the green toxic gas is very much present for the rest of the scene but does not harm either the Doctor or Ace, despite it being shown to have been lethal to the soldiers in a preceding scene. (NOTE: This error only applies the TV broadcast and the original video release; the error was noticed and corrected in 2003 for the DVD release of this Doctor Who story).
Revealing mistake: In the final episode, Glitz and the Master leave the console room while the Doctor is driven into submission, but they are quite obviously standing by the scanner screen.
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?
Continuity mistake: Near the end of episode three, Jamie starts to read the printout. At first, he is reading the printout the right way round. But when we next see him, he seems to be reading it upside down. Then the third time we see him, he is back to reading it correctly (right way up).
Continuity mistake: In episode six, the Doctor is using the Aggedor statue to fight the Ice Warriors. The door to the refinery was partially destroyed by the Ice Warriors earlier. But in every shot of Aggedor appearing or re-appearing, the door can be seen intact at the edge of the shot.