Plot hole: The Brigadier says UNIT HQ is 'a Top Secret establishment'. It is, in fact so secret that it has a large sign outside informing the world not only of its function, but also the name of the commanding officer...

Plot hole: After UNIT HQ disappears, you can see a patch of grass where the UNIT HQ used to be...but just exactly how can grass grow underneath a building?

Revealing: At various times (especially in episodes 3 and 4) you can see actor Stephen Thorne's lips through Omega's mask (and in one profile shot you can also see his jaw), yet when his mask is removed, we find that Omega has been dissipated and has no face...

Revealing: When the Doctor and Jo see Bessie in the middle of the rocky area, there is the white chalky substance from the ground on her wheels, indicating she was driven to the spot rather than being "transported" to the black-hole.

Revealing: In episode 3, when the second Doctor, the Brigadier and Benton emerge from the TARDIS, the doors are left completely open with the camera looking straight into them for a long time, revealing not only the emptiness of the police box shell, but also that there's a pair of secret doors on the opposite side to the entrance doors. These 'secret doors' come in handy during episode 4, allowing seven people to come out of the police box in the final confrontation with Omega. (Well, it is stated time and again that the TARDIS is "bigger on the inside than the outside". Now we know how that happens...).

Audio problem: When the companions are returning to Earth via the pillar of smoke, you can see and hear each person walk up the steps and then supposedly disappear. Unfortunately, you can then hear them walk down the other side of the steps..

Visible crew/equipment: You can see the reflections of the camera crew in the monitor used to display the First Doctor (William Hartnell). (This is especially noticeable in episodes 2 and 4).