I have 3 zones set up. Each gets a different number of watering minutes. Its been operating fine for well over a year however lately, all 3 zones have been going off simultaneously for the combined numbers of minutes. I’ve tried changing the watering schedules via the app and even trying to water each area separately, manually via the app but nothing works. All 3 zones go on together each time, run far too long & with all 3 zones on simultaneously, there isn’t enough water pressure for the sprinkler streams to reach many of the plants. Help? 
Start troubleshooting in the simplest form.
Physically unplug the actuators for zones 2 & 3, then disconnect 1 & 3 and finally disconnect 1 & 2 - to prove that they all can be triggered and powered from the Rachio controller.
However, if you have only got Zone 1 connected and zone 2 or 3 also activates, then this would appear to confirm a wiring issue somewhere.
A pic of the Rachio might help
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Like @championc said, there could be a wiring issue somewhere that has developed. Also, there can be a mechanical issue with the valves themselves, and when 1 zone runs, the pressure drop can actually cause the others to turn on. A rebuild with a new diaphragm can usually fix the mechanical part. I usually buy a complete new valve and replace EVERYTHING minus the actual valve body when I rebuild.
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Sounds like solenoid valve stuck open.
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