When entering the vault the picture of Elizabeth I and the 10th Doctor is twice the height of Kate Stewart with the Queen's face a good 4ft above her head. When Osgood flees the Zygons the Queen's head now barely a foot above her head, later when she looks through the damaged she is the same height.
The three Doctors have their hands stacked on top of each other on top of the big red button. There is a cut to Clara and then back to The Doctors. The Doctors' hands are now beside each other on the button.
After The Doctor proposes to Elizabeth, and is then giving his reason for not believing she is the real Elizabeth, the horse in the background changes positions between shots.
When Queen Elizabeth and her zygon doppelganger kiss the tenth doctor before running away. The fez on the eleventh doctor's head changes position between shots.
Immediately after kissing Elizabeth after getting married, The Doctor's collar is raised. In the very next shot it's down again.
When Clara climbs out of the painting, her right shoulder is turned away from the left side of the frame and she is too far away to hold it from that position, yet "her" right hand is still on the frame. A hand double must have been used to get her into such an awkward position.
In the War Council's room, The Doctor's transmissions from his TARDIS(s) are shown as floating, blue-tinted displays. POV shots are also shown of the three featured Doctors in their TARDISes that are full color with a simple frame in the corners. Those shots seem to be from no one's POV.
When the Moment is showing the three Doctors (and Clara) a projection of the final moments of the fall of Arcadia, a woman and her child maneuver slightly between the Tenth and War Doctors. If it were truly a projection that they had no physical presence in, the woman and her child would not have needed to move to avoid running into them.
When Clara clicks her fingers to shut the Tardis doors, the sound is of a finger and thumb, even though she's wearing gloves.
When The Eleventh Doctor is talking to the Time Lords in his TARDIS, there are a couple of shots where Matt Smith's script is visible on the console. The script has disappeared in future shots.
In the prison scene they discuss the sonic screwdrivers and figure they are all the same software but only updated versions. But the Eleventh doctors screwdriver and TARDIS gets destroyed, and the 'new' TARDIS creates a whole new different screwdriver, it should not be the same software but a completely new one.
Clara is able to use the Vortex Manipulator to jump to the exact time that The Doctors were incarcerated, arriving only minutes after they were locked in the tower, despite only having the year they were there to go off of.
When The Doctor is communicating with Kate via the Space-Time Telegraph, it has Brigadier Lethbridge-Stewart incorrectly spelled as Left-Bridge Stewart on the animation itself (only briefly on screen)
The Tenth Doctor always keeps his sonic screwdriver in his left inner suit pocket for ease of reach (David Tennant is right-handed). Here, he keeps it in his right inner suit pocket, for no other reason than to facilitate the "mirror" gag when the Tenth and Eleventh Doctors meet.