The best way is to ensure that the controller is grounded properly. Unfortunately, like all electrical devices, controllers are susceptible to lightning strikes and little can be done to prevent damage.

Make sure your controller is in the "off" position, remove the cover from the irrigation meter, either record or take a picture of the position of the meter then return to check it again a few hours later to see if it has moved. If the meter has moved, you have a leak somewhere in your system.