I've been experiencing the same issue with all the routes including 94 Fallowfield vs 94 Millenium, etc, etc. 86 Hurdman vs 86 Elmvale, 129 Hurdman vs 129 Blair, etc, etc etc for the past 3 years.
As a temporary fix (for the past 3 years), I've taken the liberty of manually adjusting them:
http://ottTransit.ca by looking at their last stop.