Cannot close window when click red X button

Sometimes I click red "X" button or yellow "-" minimize button on the top-left corner of window, the window cannot be closed, it likes you don't click, but the animation of the button tell us you clicked really and truly and click-event is received by it . If you move the window, then it can be closed.

It happens on any windows of any applications you opened,chrome, system apps etc., especially easily re-produce after hours of idle of app.

This problem was reported even about 10 years ago in Apple discussion,

see Re: Cannot close windows by mouse-click on red button, and Cannot Close Safari window Using the Red Button

But now it still annoys us.

What has been doing Apple?

My Mac info:

MacBook Pro (Retina, 13-inch, Early 2015)

OS X Yosemite, version 10.10.5

Processor 2.7 GHz Intel Core i5

Memory 8 GB 1867 MHz DDR3

Graphics Intel Iris Graphics 6100 1536 MB