There can be several causes for this problem, therefore, there are also several solutions.
First, you could be using a different map on the website then in the Navigation app. MRA Navigation uses the HERE/Garmin map, so I recommend you to use this map. Second, it could be due to the fact the map in MRA Navigation could be slightly more updated. Therefore, I recommend you to add about 50 waypoints on your route to prevent it from changing.