Simon's pajama top changes in the first bedroom scene.

After Evangeline has left with Aunt Adelaide, Nanny McPhee enters the children's room, and as she and Chrissie walk to the bed they pass Eric's, Lily's and Tora's beds, with the bare wood floor at the center - there is no rug. However, when Nanny McPhee leaves their room the long red and white rug is at the center of the floor, between all the beds.

Following the food fight, the amount and placing of icing on Evangeline's face changes between long shots and close-ups.

When Nanny McPhee tells Cedric, "Lesson three, to get dressed when they're told is complete," he picks up a pen and fiddles with it. In the next close-up, Cedric's hands are clasped together, and a moment later he picks up the pen and fiddles with it.

At Midgewaller & Sons, when Mr. Brown finds the card for the deceased Thadius Quickly, not only does the handwriting differ later at home, but the red swatch pinned to the card differs as well.

There is a scene where Chrissy's teddy bear has it's head cut off with a guillotine. This is a factual mistake as the film is set in the 1860's, where teddy bears weren't actually invented until 1902.

When Nanny McPhee seems to suddenly "appear" to Cook, after the children have gotten sick, you can see Nanny stand up from behind the counter, if you watch closely through the red bottle as the camera passes.

When Eric beheads Christie's teddy bear with his guillotine, the angle of the bear's head as it falls clearly reveals that the bear's head was joined to the body by a strip of Velcro (in order for it to be easily detached by the dulled blade of the guillotine) rather than having been sewn on.

When Nanny McPhee tells Agatha "goodnight", the footage of Agatha sleeping is briefly looped.

During the wedding scene, the priest is seen wearing a green stole. The proper colour stole for a wedding is white or gold. When the scene changes to snow and everything is white the priest is not wearing a stole at all.

When Simon is sitting on bed, he says "We're getting rid of her tomorrow." However the audio to this line comes a few seconds before his mouth moves.

After Nanny McPhee and Mr. Brown discuss the subjects of Simon's cleverness and Evangeline's wellbeing with Aunt Adelaide, when Nanny McPhee leaves the room a crew member's movement is seen in the mirror over the mantle.