I'm running stable Stretch 64-bit and yesterday I upgraded MATE from 1.16 to 1.20 (from backports):
sudo apt install -t stretch-backports mate-desktop-environment-extras
I wouldn't have noticed that actually but I regularly play Openarena/Quake games. Now I simply cannot rocket jump anymore (when left+right buttons pressed almost at the same time).
After running the following command I see that now 1) pressing on the wheel button and 2) pressing left+right buttons simultaneously are handled as the same event - button 2:
xev | grep ', button'
right button - button 3
pressing the middle wheel - button 2
pressing left+right buttons simultaneously - button 2
Fortunately I have Jessie installed on another drive. So I tested it there and the result is:
left button - button 1
right button - button 3
pressing the middle wheel - button 2
pressing left+right buttons simultaneously - button 1 and button 3
I'm aware that Debian has switched to libinput instead of synaptics, but there's nothing libinput related in the APT logs and everything was OK prior to that MATE upgrade.
I don't even know what package might have caused this issue in order to file a proper bug report.
I'm using now a temporary solution via .xsessionrc:
xinput --set-prop DEVICE_ID "libinput Middle Emulation Enabled" 0
P.S. I've also found something relevant (but old and archived) in the Debian Mail Lists and Bug tracker.