If you train-up your masteries in the wrong order, you could possibly cause yourself problems or force yourself into story mastery to earn points. The order you should do it is: Raptor to 3, Springer to 3, Jackal to 3, then finish off everything else. If you do it in this order you should be able to do the story and all of the content with no problem at all grabbing only the mastery points in the maps. Also, you will have to back-track to past maps to pick-up mastery points you previously could not get until you unlock the correct mount and train the correct skill (i.e. Springer 3 is required to get the Glint's mastery point in the Oasis map, and the Manta is required to get the quicksand mastery on the same map.) Don't try and finish off a mastery, like training Raptor 4, until you have unlocked all mounts and trained Raptor, Springer, and then Jackal to 3.