I don’t have much recent experience with the PDE Toolbox, but your ‘rect’ assignment is missing the last two y-coordinates for your rectangle:
rect=[3 4 -1 1 1 -1 -0.5 -0.5 # #];
where the ‘#’ indicate the missing coordinates.
In the documentation for Create CSG Geometry at the Command Line, the ‘3 through 6’ and ‘7 through 10’ refers to the vector needing four x (in elements 3-6) and four y (in elements 7-10) coordinates to define the rectangle’s corners.
EDIT — The error, ‘Index exceeds matrix dimensions.’ means that the relevant PDE routine is looking for the last two elements in your ‘rect’ vector and can’t find them.
