Sometimes the remote control agent will simply lose mouse/keyboard control. You can still view the session, but you are no longer in control. A disconnect/reconnect is the only solution.
The remote control agent can have issues with super-high resolution video cards. It causes the mouse to be "off" by a few inches on the screen. You have to ask the end-user to adjust the monitor to a lower resolution, then reconnect.
Huge patches can be an issue because the end-user needs to first wait for the patch to DL, then install. They often grow frustrated and reboot while the huge patch is still downloading. It would be nice if it pre-pushed larger patches in the background, then installed it. We've found a manual way to pre-copy the patch files into the end-user's target directory, but this workaround is not ideal.