My buddy Dave in Tempe had the exact same problem with his Rachio last spring. He tried to adjust a zone from the physical box after setting the schedule on the app. The whole system just locked up and watered his cactus garden for three hours straight on a Tuesday afternoon. He had to do a full hard reset, pulling the unit from the wall for a minute, to get it to listen again. Now he only uses the phone app for everything and it works fine.
Did you check if the sprinkler head itself was set wrong? Sometimes the smart controller is fine, but the physical zone is aimed at the patio. What brand of controller did you even program for this mess?