You have a couple of avenues open for a possible solution. If this is the only thing you are using your Pi 3 for you can turn off the Raspbian desktop and start up the kivy app as a full screen app. When run from the command line w/o X a kivy app will automatically start up full screen.
The other thing you should check is your .kivy/config.ini file. In the Input section make sure you don’t have extra entries for the mouse.