Continuity mistake: When Tick Tock freezes Rebecca and Cecil, they are in one position, and when they go to the close up of them frozen, they are in a different position. When it zooms back out again they are in the first position. Also, when they are frozen moving on the conveyor belt, they are back in the position they were in on the close up shot.
Continuity mistake: When the house is attacked by the Timekeeper's goons, the kids escape to the panic room through and elevator in the fireplace, and the empty fireplace/elevator is replaced with a fruit basket. When the goons search the living room, the basket is now gone.
Continuity mistake: At one point, the Timekeeper threatens the spies by extending a blade from his arm. When the shot shows the Timekeeper, the blade looks like an ordinary sword, but when the shot changes to show our heroes, the blade looks like a clock hand. This happens twice in the scene.
Continuity mistake: When Cecil, Rebecca, and Argonaut escape the OSS lounge, Argonaut spills a large puddle of ink (with one leg up) to fight the OSS Agents. The ink was spreading very close to his legs. In the next shot you see Argonaut running without paw prints on the floor. He had to step in the ink if it was so close to him. At the same time, the puddle has gotten smaller than before.