It is understandable that text selection using the mouse is tricky when the terminal is scrolling because of command output being generated. It is much less intuitive that this is also the case when you have scrolled back up the history, e.g. to see (and copy from) the first output generated by a long-running process. I do not know if it's possible to maintain a reliable offset into the scrollback buffer corresponding to the mouse pointer position when the terminal has been scrolled back and text is being appended to the buffer. It not, it may be less frustrating to disable text selection (when both conditions are true, or even while output is being generated and the terminal isn't scrolled back) and sound the bell instead.
I've just tested this on konsole from git master and I cannot reproduce. Can you please test and confirm if this bug is still valid, thanks.
I've been running #ac8799ba587e50cd68e4c676f990274c22e41280 for a while now, and can confirm that it appears the issue has been solved.