In the current HEAD, when I have open a program that uses the alternate screen and is not written with mouse support, I am able to send cursor up and down events by using the mouse scroll wheel, per commit 353d1825d5a3a6efb1c3c71d9afbb96ba57cc948. However, it seems that if I left-click within such a pane after having scrolled, the left-click down causes an additional scroll event (which is translated to one or more cursor up or down keypresses), and the left-click up causes yet another. The direction of the scrolling/cursor movement is the same as the last one triggered by actual scrolling, and the number of lines matches the number of lines of the last scroll event too (3 for normal scroll-wheel use and 1 for scroll-wheel with shift held down).
In addition, if I have not scrolled in the alternate-screen app, the "echo" event mimics whatever scrolling I last did in another window or pane, even if that window/pane is not using the alternate screen. Seemingly the only time cursor movement is not triggered by clicks is just after starting the tmux client (restarting the session/server doesn't seem necessary), or after running it for a while but without doing any scrolling.
I have experienced this in tmux HEAD (f8481f9) in iTerm2 184.108.40.20640518 in OS X 10.9.3.