I may have found a work-around (or the cause of the problem).

I had the focus mode for windows set to "Sloppy". Changing this to
"Click" has seemed to resolve the issue. I am not sure if "Mouse" also
causes the same problem as "Sloppy", but I'm not willing to try, I just
enjoy having my mouse work as normal.

Here is where I changed the setting:

Tweak Tool -> Windows -> Focus Mode

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https://bugs.launchpad.net/bugs/1316873

Title:
  Left mouse button stops working

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https://bugs.launchpad.net/ubuntu/+source/xorg/+bug/1316873/+subscriptions

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