It is a problem when players waste badges on waypoints you aren't doing. We had the problem and it took about 2 years to get people to stop doing it. I start as soon as I determine the path we are taking (about 2 days after Beta is done) and hammer it into them as much as I can. I put it in messages and in chat. But since I plan the path, in my calculations, I exclude the usual offenders. In other words, if I think player X is going to waste a bunch of badges because he/she never pays attention, I just leave them out of my figures. Then, if they manage to put badges where they belong, I don't get upset because it's a "bonus." That's how I kept my frustration in check, especially at first. Now we are doing this FA and so far, no lost badges.
Along that line too, since we generally do all the waypoints in stages 1 and 2, I still insist on people doing them in the order I say. Why? As I explain it to them, it's practice. No team goes into a game without practicing all the aspects of the game, even if they aren't needed in most of the game. For instance, you don't do your endurance routines for the first quarter of the game, but for the last. So we practice following orders through the whole game because in the last third we will need to do it right. That explanation, btw, seemed to have a really good impact. Things went from not improving very fast to a great improvement.
Finally, you could make it mandatory they read their mail. I send out a "response measure" every few months to see who is and who is not reading their mail. The ones who don't, get a private message requesting (gently) that they do. This, too, has improved the FA.
AJ