Pretty sure most of you already know this but for those who don't: you have two clipboards in Linux.
One is the traditional clipboard where you copy with control c and paste with control v.
The other one is when you highlight text and use the mouse middle click to paste text.
How do middle-click-to-paste and middle-click-to-scroll conflict? In Firefox I can click-to-paste if the cursor is over an input field and click-to-scroll anywhere else. Never had any problem with this behavior.