That CTRL+SHIFT+C thing in Gnome Terminal/Ubuntu (and some others) has driven me nuts for years!!! yes, I get that CTRL+c means something different in the context of shell execution. But it's still maddening.
Middle click to paste is an unrelated thing that drives me up the wall in Linux. Many of the programs I use on a daily basis have specific actions triggered by a middle click that I use often, but if I miss my target and hit a text area instead, it injects whatever I had in my clipboard into the text, often without me realizing it until later. (In one instance, my clipboard contents made it into an email I sent out. Thankfully, it was minor enough that it just looked like a typo, but it could have been much worse.)
Unfortunately, I'm not aware of any way to turn off this behavior.