Madeline is a Reality Warper
The other 11 girls Took a Level in Dumbass while Madeline stayed at the hospital in the first TV special ("First we brush our bread, and then we...break our teeth?") because they are physical manifestations of Madeline's imagination, and didn't know how to function without her. Madeline also created Genevieve to save her from drowning, and granted Genevieve the relatively high intelligence she demonstrated during class. Pepito also sprang forth from Madeline's imagination because she wanted a cute Spanish boy to live next door.- But if she were a reality warper, she wouldn't have let herself get appendicitis in the first place. And the girls were probably acting dumb because they were shaken up by the idea of their friend getting surgery.
In the movie-verse, Carly Simon attended the school at one point.
The song "In Two Straight Lines" is sung from the perspective of one of the girls (who isn't Madeline). Moreover, she was born in 1945, while this movie has a Setting Update to the 1950s, which would make her old enough (just about) to be in (any, let alone this) school during that time. Fred's not dead
To clarify for people who haven't seen the live-action movie: "Fred" is a chicken bought for dinner by the cook Helene – Madeline names and becomes attached to the chicken, and when dinner is served that night, Madeline leads the other girls in refusing to eat "him." But how could Helene be so callous as to kill and cook a chicken she knew Madeline saw as a pet? The answer: she didn't kill him. She knew that would make Madeline sad, but she did still want to make chicken, so she bought an already-dead chicken. She just didn't get the chance to tell Madeline in time. Marie herself isn't an angel, but she knows a few angels personally.
I've seen lots of speculation that Marie from "Madeline's Christmas" is an angel. While she doesn't have wings or any overt powers, she does cure everybody instantly with her porridge and the angel at the top of the Christmas tree has her face. Maybe she knows angels personally and it was those angels who gave her the porridge recipe. Sugar Dimples will produce a Madeline TV special when she grows up.
In real life, Shirley Temple produced a Madeline adaptation as part of her Shirley Temple's Storybook series in 1960. In the later Madeline cartoons, Madeline befriends the Shirley Template Sugar Dimples. She also befriends an artist named Ludwig, who eventually is shown writing the first Madeline book. Within the world of the cartoons, the events will play out more-or-less like real life. Sugar Dimples will grow up to host her own Storybook TV series and one of the episodes will be based on Ludwig's book – possibly with the real, grown-up Madeline on hand as a consultant. In the cartoons, Sylvie and Simone are twins.
This probably isn't the case in Season 3's continuity, where Simone is renamed Ellie and has her skin and hair darkened. But in the original specials and earlier series episodes, they have the same light olive-brown hair color, with the only difference being that Sylvie's is long while Simone's is cut in a bob. They're also shown standing next to each other several times in the original special. The series episodes are in Anachronic Order.
This would explain why Genevieve is inexplicably absent in some episodes. They take place before Madeline's Rescue. It also explains away one apparent Series Continuity Error: the fact that Madeline at the Louvre shows Madeline learning to paint for the first time, when in the earlier Madeline's Christmas she painted a picture of the Nativity. ...at the Louvre is also an episode without Genevieve, so it must take place earlier than both Madeline's Rescue and Madeline's Christmas. It might even take place before the original Madeline, since at one point in the original special, Madeline sings about the Louvre and The Mona Lisa as if they were already familiar to her.