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.
More details here.
I actually like the feature but could you explain how you disabled it? I've tried to merge all three clipboards into one a few years ago and couldn't make it work
KDE has the option to disable middle click paste, so I do that. Out of sight, out of mind