Creating two simple circles and making them one object. Then doing a boolean to subtract two rectangles that are centered horizontally, changes the height of my Circles. View GIF for more details.
Bug might be a little exaggerated, 0.008mm (in my test) is more of a rounding error in calculating the “new” shape 
But yes, it should be 100mm in height. Fortunately, we have no laser that has a problem with this deviation.