This story is a sequel to Spearhead From Space, which was shown the year before. Despite being produced only a short time later, and written by the same writer (Robert Holmes) there are elements of this new story which don't quite match up with the earlier one.
In Spearhead, there is no indication of any Nestene sphere being unaccounted for. The only one missing is the one that poacher Sam Seeley has found, which the Autons eventually track down. Yet in this story there is an intact sphere that was somehow missed.
The Autons in the first story could not, or would not, speak, but they can and do here.
The Nestene only needed the Autons in the first story to get their invasion plans up and running, so why not do the same again? Why do they need the Master?
And why does the Master need the radio telescope, when the Autons didn't need anything like this the first time?
Despite everything that happened in Spearhead, why on Earth would the Brigadier allow an intact Nestene sphere to go on show at a museum? How did the museum even know about it, if UNIT and its activities are supposed to be top secret?
Despite the Autons' previous use of a plastics factory, UNIT take rather a long time to start investigating them here. When it becomes clear that Jo must have encountered the Master at one of the ones on her list, why does it take the two suspicious deaths to attract the Doctor's attention to Farrell's? Surely Jo's list couldn't have been all that big?
Why does the Master go to the circus? It is a colourful plot location for the first two episodes, but is then discarded once the action moves on. Why did the Master not just go straight to the plastics factory and start making Autons there immediately? The kidnapped scientist, Phillips, could have been hidden there just as easily (if not better - as there are Autons there). And why kidnap the Phillips in the first place?
He serves no purpose, other than to actually become unstable and put the Master's plan at risk.
The Master's TARDIS is not very well protected, and the Doctor is given ample time to get inside and steal the dematerialisation circuit.
Mind you, the Doctor leaves his TARDIS door open all the time, so why doesn't the Master do some sabotaging of his own when he breaks into UNIT HQ?
The sequences at the radio telescope cabin in Part One throw up all sorts of issues.
It's a great pity that we never got to see the scene of the Master and Phillips having to clamber out of the radio telescope cabin window - as that's the only way they could have got out after the Master had set up his trap.
Why have the trap in plain view of the window? And why on Earth doesn't the Doctor check through the window, rather than blindly edging the door open as he does? He doesn't bother to warn the Brigadier, Jo, Mike Yates etc. and get them out of the area before he tackles the bomb.
UNIT have been called in because two scientists have gone missing, yet no-one has bothered to check the cabin - where the two men work. If they had checked it, then did the Master pop back again afterwards to set up his bomb trap?
The Master's bomb would have made a right old mess of the radio telescope had the Doctor failed to prevent it falling.
That's the radio telescope which is vital to the Master's plans.
The civil servant Brownrose comes to UNIT to tell them about lots of unexplained deaths in the region. Did every single one of these people really die on their own, with not one witness to see them collapse seconds after holding a plastic daffodil? Surely the flowers would have been dropped on the floor as the person dies - giving a clue to the authorities that they were involved, if every corpse had a daffodil next to it?
A fluff between Pertwee and Richard Franklin - when Yates says he had "gone to fetch some cocoa", the Doctor responds "fetch a tin of what?". No-one mentioned a tin of anything.
Director Barry Letts is happy for us to see the troll doll being blasted to bits by a handgun - but can't bear to let us see a solid rubber toy being cut open. He later stated that there were complaints from parents about their children being afraid to take their teddy bears to bed at night in case they came to life and throttled them.
Just what was the Master's plan here? Did he want to see the Earth destroyed by the Nestene, or did he want to conquer it for himself? If the Nestene were going to destroy the planet, why did he continue to co-operate with them when he knew that he no longer had his dematerialisation circuit - and so would be stuck here as well? He has lots of opportunities to get his circuit back, but fails to take any of them.
Why did he not just allow the RAF to bomb the coach? He would have got rid of the Doctor and sacrificed only a handful of Autons, whilst he could have sneaked off to the radio telescope - a location UNIT haven't thought of until the Doctor warns them.
And did it really take the Doctor to point out to him that the Nestene might not want to treat him any differently to anyone else on the planet? When the Doctor does this, he switches sides amazingly quickly. There is not even the slightest hint of an argument about this.
At the conclusion, the Doctor grins as he says he's looking forward to his next meeting with the Master - despite the fact that hundreds of people have just been killed.
(Barry Letts' boss objected to the original line: "Until I kill him, or he kills me..." as being too much of a downer).
Behind the scenes, a single location shoot was the cause of many problems. Nicholas Courtney suffered a panic attack and could not film, so an extra took his place. You can spot him as he is wearing white socks, which the Brigadier would absolutely never do. Then the stunt involving Terry Walsh's Auton policeman went slightly awry, and he tumbled down the slope far further than intended after making contact with the car. On the same day, Katy Manning injured her leg tripping over some rocks (she was as blind as a bat without her spectacles). Production Assistant Nick John, brother of recently departed companion actress Caroline John, joked that as she had only just joined the production she could be easily replaced - something which upset Manning, and Jon Pertwee in turn.
The Auton policeman caused a complaint from the police, arguing that youngsters were being encouraged to approach officers if in trouble - not be put off by them in case they were Autons.
His first chance to direct a story now that it's in colour and he's in charge, Barry Letts is over-zealous in his use of CSO. The backgrounds to the museum, Auton laboratory, and Mrs Farrell's kitchen are obviously photographic - the latter looking the size of a barn.
When Robert Holmes later went up for the Script Editor job on Doctor Who, he was told by Head of Serials that some idiot had once written a story which generated lots of complaints from parents and police, and he should try and avoid this sort of thing. He elected to keep quiet about his involvement...