When you have units on follow they have two modes: moving to get to you, or waiting for you to get out of range so they can revert back to the first mode. If you mass teleport, use a waygate, town portal, blink, or anything of the like while they are in the 'second' mode, they stop following you. This is true of all maps, and unfortunately there is nothing I can do about it, because it is a programming bug that is beyond my reach. Only blizzard can fix it :-/
However, it is also true that this map kind of draws out this bug a bit more than most maps, due to the long running distance but short flying distance to the waygates.
The only possible way to 'cut down' on it is to stack boots of speed, so that your flying units spend more time in that first mode, and thus are more likely to be in it when your hero hits the waygate. Additionally, you could 'waypoint' the waygates on all of your unit-making buildings, forcing them to take the long way - that 'could' help a little as well... But I'm afraid there just isn't anything I, or anyone except blizzard, can do about this...