Are you talking about X/Y squareness or X/Z squareness?
Anyway if you want an angle to be 90° (=if you want your machine to be X/Y-squared), then you measure X and you measure Y and then, with knowing the angle you want (90°), you compute the diagonal that has to be there. Then you check by measuring the diagonal.
Remember that if one diagonal is shorter than the computed value, the other will necessarily be longer. So to ensure a 90° angle, it will be enough to shift one axes’ ends until the diagonals are identical.
One simple way to ensure squareness of X to Y on the machine is ensure by measuring that both diagonals are identical. It’s as simple than that.

I’m ~80% sure this is out of square, though it could also still be a parallelogram. Here’s one example piece I tested yesterday where the tilt is most obvious visually. I did cut a square test pocket and visually it has a similar tilt to it. The pocket is roughly equal on the diagonals and flats according to my quick check with some calipers.
At first sight, this looks as if the letters are rotated in comparison to the rectangle.
If we have rotation here, then it is not a X/Y out of square issue.
Do I understand it right, you milled the letters, or the shape of the rectangle or both or what?