- Continuity: Following the food fight, the amount and placing of icing on Evangeline's face changes between long shots and close-ups.
- Continuity: 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.
- Crew or equipment visible: After Nanny McPhee and Mr. Brown discuss the subjects of Evangeline's wellbeing with Aunt Adelaide and Simon's cleverness, when Nanny McPhee leaves the room the crew member's movement is seen in the mirror over the mantle.
- Continuity: When Evangeline shows Nanny McPhee the book she is learning to read, the book mark changes between shots as Nanny holds the book up.
- Continuity: When the Brown kids are making a mess in the kitchen, the bites in the large round bread that Sebastian holds change, and actually become fewer.
- Continuity: When Mrs. Blatherwick sits in the rocking chair in the kitchen, before the "mouse" races across the floor, in the first shot her left hand lies on her belly, with her right hand over her left, patting it gleefully. When it cuts to a close-up, her hands are in the opposite position.
- Continuity: When Eric, Tora and Aggy are getting ready for bed, Simon walks in and mocks, "And since when have we decided to do what we're told?" The towel to his right (viewer's left) is rumpled up, yet hangs straight in previous and following shots, then is rumpled again.
- Continuity: When the tarantula is crawling on Selma Quickly's hair, Cedric dives onto her. In the first shot his hands are around Selma's neck, as he is falling on top of her, but in the next shot his arms are wrapped around her waist with her arms dangling over his.
- Continuity: 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.
- Audio/visual unsynchronized: 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.
- Continuity: 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.
- Revealing mistakes: 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.
- Continuity: Simon's pajama top changes in the first bedroom scene.
- Continuity: When Nanny McPhee's magic is transforming everything for the wedding of Cedric Brown and Evangeline, Cedric's tan jacket appears and disappears between shots.
- Continuity: When Nanny McPhee entered the nursery to put the children to bed, her mole is missing before the close up SFX disappearing shot.
- Continuity: Just before the wedding when Ms. Quickley was talking to the children, she takes the rattle away from Aggie and breaks it in half with the handle in her right hand. I the next shot,the broken pieces have switched places and the handle is in her left hand. Then when there are two pieces not zoomed in, the handle has returned to the right hand.
- Continuity: During the food fight scene, Aunt Adelaide gets a slice of cake fired at her face, leaving a thick layer of light green color. Then next scene, Aunt Adelaide is walking away, and the frosting is a dark green color.
- Continuity: Throughout most of the movie, Sebastian is missing one of his front teeth. However, in the scene where he's hiding behind one of the chairs while his father and Mrs. Quickly have tea, his missing tooth has grown most of the way back in. Later in the movie, the tooth is missing again.
- Continuity: When Cedrick starts to plump the cushion for Mrs quickly, in the tea scene,it changes from a brown tapestry cushion to a bright yellow cushion.
>>> WARNING: Here Be Spoilers <<<
Goofs below here contain information that may give away important plot points. You may not want to read any further if you've not already seen this title.
- Continuity: SPOILER: In the end Tora is holding Agatha when the shot changes to show Nanny McPhee repairing the rattle, but when the rattle is given to Agatha, she is in her basket, even though the wedding is still going on.
- Continuity: SPOILER: At the wedding, when the characters are having a food fight, the bride and groom figurines on top of the wedding cake are knocked off. In the next shot they are standing back on the cake.
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