Someone tied the two zone wires together somewhere or from a short. Most controllers can handle up to two solenoids per zone without any problems. On irrigation systems one side is a common wire (24v ac) and usually all the have one side of the solenoid tied together by daisy chaining the connections for all solenoids. With one trench all wires go in the same treach feeding all valves. Perhaps at one of these replacement solenoids someone tied two zone wires together. At times a zone wire is spliced at one valve box to make it to the next valve box. If the wires are the same color and sometimes the old wire nuts come loose, someone tied them together.
On controller 1 disconnect the zone wire with the problem and turn on controller two. See what happens. Then do the opposite. This should prove a short exist.
At both valve boxes open the up and check the wiring. The two solenoid wires, the common side (usually white) may have three wires, one to the solenoid, one wire in and one wire out to the next valve box. The other wire will have only two wires, one for the solenoid and the other from the controller.
