I ran into an issue where my Logitech Master MX 3 mouse wouldn't scroll within iTerm 2 if the window had focus. Oddly enough, you could still scroll the window if it didn't have focus.
After some Googling, it looks like there's a simple fix: uncheck the "Secure Keyboard Entry" option from the iTerm 2 dropdown.
There may be other solutions but this one worked for me.