There does seem to be a bug as you can get within a meter of the plane and still the waypoint won't complete.
The only way I can do it is this.
You will have to put yourself in a group by placing this line in your units init box.
name the plane and place this line in it's init box
Next create a trigger and name it trig1 and setup as follows
player distance planename <=10
You will have to change the number after in deletewaypoint to match the one that isn't working.
deleteWaypoint [grp1, 4]
What I'm doing is using a trigger instead of the waypoint and when it becomes true it deletes the faulty waypoint.
Has anyone got a better way of doing this?