First, waypoint links in chat should include which instance of a zone they go to. Someone in guild chat links that they have a bounty target, the guild should not get scattered to three different versions of that zone when they take the waypoint link.
Likewise if someone posts a waypoint link in chat asking for help with an event or skill point, people jumping to that link should be in the zone the poster asked from. They shouldn’t arrive and assume that since they don’t see the player that asked, that the player got frustrated and left, only to see the player asking again later.
If you click on a waypoint link and cannot go to the same zone as everyone else that is clicking on that waypoint link, then you should get a message much like the overflow zone messages before and the option to enter the correct zone when possible. This way you at least know not to waste your time looking for the rest of the players you were expecting to meet in this zone.
Second, when multiple instances of a zone are active it should be visible. Other games with the concept have appended numbers to the end of the zone, so you see that you were actually in divinity’s reach 3 instead of divinity’s reach 1. You could ask players which one of multiple zones they were in, or ask for them to link a waypoint so you could get to their zone once you realized they were in a different instance of the zone than you.