Some atoms not registered as children properly
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RyanR712 commented
If atoms are placed at the very edge of cuts' ellipses such that the corners of their bounding boxes are outside of the ellipse, they are not registered as that cut's children, even if they appear to be visually.
To reproduce, tick the Show All Bounding Boxes checkbox for atoms, and position one inside an existing cut such that one of the bounding box' corners are a tiny bit outside the ellipse. Then check the formula string to be sure.