Hexagon with different sides measurements

When you use the numeric edits toolbar to change the width and height you are changing the geometric size of the shape. Since the top and bottom are sides of the hexagon whereas the left and right are corners, you are stretching the shape asymmetrically.

You can avoid this by changing the size of the hexagon in shape properties. Note that for all polygon objects that the size of the polygon is defined as the size of a circle that fully contains the polygon. Meaning the polygon is inscribed into the circle.