For some time both my Macpro and Macbook would have windows that I could not close or Safari would have tabs that I could not close.
Turns out the problem is very common and frustrating. The solution is to change the Double Click speed to something rather high in trackpad preferences.
Note: this problem can be reproduced by clicking between the Red and Yellow buttons on the top left of a window. Those buttons are now non responsive till the window is clicked again – say by moving it using the title bar.
Updated: May 1: after 24 hours use, problem has not recurred.