Same issue here, didn’t get credit for zone 2 and now I can’t enter zone 3. Did you guys wait for the timer after completing the zone? I exited the instance as soon as I defeated the boss and looted the chest, and I think that may be the issue. When I did zone 1, I waited for the timer.
Edit: I went through zone 2 again and waited for the timer to end, and I did in fact get the achievement for completion upon being taken to the next zone. However this issue is still a huge inconvenience, and I hope there’s a fix for it in the future.