Why is screencapture taking the screenshot of the desktop image and not the windows on top in Catalina?
Instead of screencapture -s ~/Downloads/screen.png source where -s is for


  Only allow mouse selection mode.


try -w. It will show a camera icon and wait for you to select a window. Hit esc to cancel the process.

screencapture -w ~/Downloads/screen.png



  -w      Only allow window selection mode.


I cannot say why -s doesn't work, but on Mojave, the man page says 


  The screencapture utility is not very well documented to date.  A list of
       options follows.