First of all, Eric Saward himself has been saying almost from day one that he doesn't think much of his own story - despite it doing well in polls at the time. It's generally felt that there are too many subplots, like the whole "Assassination of the High Council of Time Lords" plan.
The Daleks have hidden their samples of Movellan gas in 1980's London, in a building which is sure to be investigated by workmen - and indeed this is exactly what has happened. Workmen find the blue cannisters, and promptly call in the army as they think they're probably unexploded WWII bombs. The Daleks have time travel capability and are actually hiding the cannisters in time as well as space, as they're based in the far future.
Surely that warehouse isn't a terribly safe location for such important objects - they need Davros to examine the samples to find an antidote as they're being thrashed in their war with the Movellans - and surely they could have checked how secure their hiding place was at this point in history. Or was it always the plan that people would find the cannisters? If so, why?
Apparently it's all a deliberate ploy to trap the Doctor - but how would the Daleks know that he would fall into their time tunnel? It happens when he's in their far future.
Tegan is left prisoner at the warehouse. Why not transfer her to the Dalek ship as she's also be duplicated? Stien specifically states that the Time Lords - who they want to assassinate, remember - would be suspicious of the Doctor without his companions. When they do finally despatch her there, she's left free to wander around. No Daleks, or even one of Lytton's men, waiting for her, despite her apparent importance.
Why use Lytton and his mercenaries if the Daleks can create their own duplicates, who look exactly like the people copied?
The duplicates have to be mentally conditioned - so why not just do that to the originals?
Why do only some people fall down when the time tunnel is operated? Why would you have a device which knocked people out every time you switched it on?
The Daleks fail to properly guard the self-destruct chamber, so serves them right for getting blown up when they hang about the space station instead of just grabbing Davros and flying away. Davros claims he needs to be near his cryo-chamber, but the Daleks ought to have (a) thought about providing such a thing themselves on their ship, or (b) just ignored him as they don't trust him anyway.
How did Davros manage to get that mind-controlling drug dispenser installed in his chair if he's been frozen / imprisoned / tried / frozen for the last 90 years? Was it always there? If so, why not use it earlier on Skaro?
He appears to be surprised to hear about the stalemate between his creations and their robotic foes - even though he saw it in action in Destiny of the Daleks.
Not something wrong as such, but the actors playing the duplicate soldiers compete to have the most dramatic death when exterminated. They really milk their deaths for all they are worth.
Dalek death rays don't always appear on screen in the final episode.
Leela doesn't appear on the flashback sequence of companions - a mistake, or has the Doctor deliberately blocked her as she's on Gallifrey and might be able to foil that assassination plan?
Probably a mistake...