Wow Mike, thanks to your comment I realized I had the exact same problem
with my Logitech M210 wireless mouse. I notice that it seems the
majority of other reports here also are reported using Logitech mice, so
this particular issue may very well be a chronic Logitech mouse problem
and not software related at all.

Comments like these make me even more suspicious that this is hardware related 
and not software related:
"Middle button on my M557 BT mouse resumed normal expected functionality, no 
specific action on my part, even though I could swear it didn't work on firing 
up the PC this morning." -The faulty switch probably got knocked back into 
place.

"the middle click now occasionally works. I would guess that with the
chance of 1/2-1/8 the click works. In the remaining cases it does not."
-Since the click can register with extra force, this would explain why a
user might see it working sometimes and not others.

"The failed mouse device was a "Logitech USB Receiver", USB ID 046d:c517
On runtime I attached another Logitech mouse, USB ID 046d:c52f, running 
absolutely fine in this regards." -another mouse works fine

In sum, I think this issue likely has nothing to do with the Linux
kernel or any other package, and may be a candidate for closure.

This shouldn't be confused with the mouse scroll issue that John M
reported, which does appear to be software related, but that should be
filed as a different bug as it has to do with the scrolling function of
the wheel and not the middle mouse click.

Probably not of interest to anyone, but I am going to try taking my
mouse apart to see if I can bend something back into place.

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https://bugs.launchpad.net/bugs/1581088

Title:
  Middle mouse (wheel-click) button stopped working after upgrade to
  16.04

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