These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Big Lipped Alligator Moment: In the sequel, the uncle lets all the farm's piglets out of their pen and the children have to hunt them down, and Nanny McPhee decides that dragging out this task further will teach them a lesson in teamwork. Which justifies making the pigs harder to catch by granting them some speed and agility, but seriously... synchronized swimming?
In the sequel, the two boys headed to the War office in the capital to ensure they had proof that the Disappeared Dad was still alive... yet they hear the news and immediately leave empty-handed? At least grab the paper ribbon code thingy from the radio guy first...
The sequel's climax. Why do they have a manual explaining in detail how to diffuse an enemy bomb in plain English, and why does that bomb have a timer if it is supposed to explode on impact?
Fridge Brilliance: Because Nanny McPhee made it happen with her magic. It was lesson four — To Be Brave.
Baby in the stew. Th-the baby. The baby... sure, she didn't actually go in the stew, but the chicken boiling up and gah... Probably rates a What the Hell, Hero?, considering the sister will have to remember how she was almost forced to boil a baby alive.
What Could Have Been: On the commentary, it's mentioned that the baby originally was supposed to be bouncing in the pot as it got hotter and hotter...they scrapped that when they realized that would be a little too disturbing.
The wriggly black goo Nanny McPhee gives to the children as "measles medicine".
Miss Topsey and Miss Turvey and their threats about what they're going to do to Phil in the sequel film. It's even worse in both the original British version and in the novelization. I mean, showing up in nurses outfits, planning on scooping out a man's insides out while he was handcuffed with no escape while he was still alive...then stuffing him and sticking his dead body on a spike as a warning to everyone else? And actually brandishing a huge scooping spoon thing at one point.? That doesn't sound like a kid's movie to me. I mean... I thought I'd see that in Saw.