Theory:Doctor Who video game discontinuity and plot holes/City of the Daleks


 * When the Doctor spots a burnt newspaper in the ruined London with its story about the Dalek invasion, the picture is of the Time War Daleks rather than the new Progenitor Daleks.
 * The new Daleks may have used inferior Dalek models to make up numbers.
 * The four Daleks seen in the newspaper are the Cult of Skaro, and they were stranded on Earth in the 1930s (Daleks in Manhattan/Evolution of the Daleks) so perhaps a photo of them was located and used for the newspaper artical instead; afterall it is likely that nobody would be able to take a picture of the Progenitor Daleks while they were destroying the planet as swiftly as described by Silvia. A photographer would likely be exterminated.
 * When the Doctor and Amy travel to the ruined city of Kaalann, all the ruined Daleks look like the new Progenitor Daleks rather than the Time War Daleks, as does the ruined Emperor.
 * It is possible that the "new" Progenitor Daleks aren't actually new. For all we know, a small number could have existed on Kaalann during the Time War, and all were destroyed at it's climax. With the Progenitor, Time War-era Dalek survivors were able to restore them.
 * The Progenitor Daleks may have also reclaimed Skaro before they even found the Eye of Time. They could have set about rebuilding Kaalann - complete with new Dalek casings and the Progenitor Emperor's cradle - but then they were forced to put the reconstruction efforts on hold as they were drawn into another war (like the war depicted in The Only Good Dalek for example). That war could also have made its way to Skaro, explaining all the broken casings seen by the Doctor and Amy during ACT THREE.
 * In a short interview given in Doctor Who: The Dalek Handbook, Gary Russell suggests that with the Daleks' time meddling with the Eye of Time (which, he states, they recovered from the Time War) and with the time cracks, the approaching collapse of reaility and then the Big Bang Two (The Big Bang), any amount of Dalek history could have been rewritten and changed.
 * When the TARDIS leaves Earth at the end of ACT ONE, its doors are facing in a different direction to when the TARDIS landed.