WMG / Madeline

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 Genevive to save her from drowning, and granted Genevive 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.

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.
http://tvtropes.org/pmwiki/pmwiki.php/WMG/Madeline