Let me start off with saying that I do try to use the mouse in vim as little as possible, but there are times that I will end up using it to click around or highlight something.
With that said, here's the problem I'm having. For the most part, I'll have my terminal (terminator) maximized on one of my monitors and I'll generally have vim open with 2 or 3 windows split vertically on it. The problem comes up when I click on the right-most window; it will instead move the cursor to the left-most window. Because I rarely click, it really throws me off when it's not the expected behavior and I can never get used to it.
I searched around for what the problem could be and found that there was a problem with xterm and mouse clicks past the 220th column in the terminal. Supposedly, it has since been fixed. I'm able to more easily test the problem by just opening vim in a max size terminal and creating a ~250 character line. I can't click on any character past the 220th column. After searching around, I found that many people suggested setting "ttymouse=sgr" in .vimrc. I tried that, but it didn't change anything.
I did mention that I'm using terminator as my terminal. I'm not seeing this behavior in gnome-terminal, but I would really prefer to stick with terminator. I'm not super familiar with how mouse integration works with programs inside the terminal, but I imagine something about the terminal capabilities is different between terminator and gnome-terminal.
I'm running Ubuntu 14.04 LTS.