As far as I can tell, the ALERT button isn't instanced (kind of... bear with me), but the alert itself is.
For example, you're in Regulus block, instance 4, along with another 30 players. If several of those players decide to go into a Red Alert, you've got 3 instances open of the Alert itself (not of Regulus, this is important):
Instance 1, 5 players (I think RAs have 5 slots... it may be more, but the point is, it's full )
Instance 2, 5 players
Instance 3, 2 players.
You click the button, and it puts you into the first Red Alert with a free space (in this case, instance 3).
The problem is, the Alerts with 5 players in will probably finish first. If instance 1 gets completed, but a player stays in the map, it's still a viable map to put new players into. It still exists.
Instance 3 may still only have 2 players in it, and still have Borg to kill, but while there are completed instances like instance 1 WITH PEOPLE IN THEM, other players will get dragged in too, because the game knows it's open but not full.