Revealing mistake: In the hotel meeting scene, the Grand High Witch tells the witches they can take their wigs off. When we see the newly bald witches, it is particularly obvious that only the foreground witches are ladies with bald caps - the rest of the witches are bald men. (00:30:10 - 00:31:00)
Revealing mistake: Of the witches that are bald, the make-up's bald cap is much too obvious on some of them in many shots.
Revealing mistake: The grandma, who has a missing pinkie, clearly has it in some shots, and in some scenes it is clear she is bending it behind to make it seem as though it is missing.
Revealing mistake: When the mouse is pushing the potion down the spoon handle towards the soup, both the bottle and the spoon turn green due to the chroma screen.
Answer: She probably didn't know about her master plan, just about turning kids into mice. Most likely she thought they'd be kept in locked cages and held prisoners.
During the meeting, Miss Ernst says that every child in England must be "Rubbed out. Destroyed." A clear indication that she was talking about killing the children after they get turned into mice but, Miss Irvine doesn't seem shocked or upset after hearing this.