Well, even though Psychic Terrain prevent high-priority moves, it doesn't change the speed stat of the Pokemon whatsoever. So, maybe the opponent just used it's Latios' EVs in SpAtk and SpDef and not much in Spd. If you raised your Zygarde's Spd with EV's, nature, or IV's, it's not unusual on why it may be faster.
Hope I helped! :)