This can happen with overlapping sections of a route, where it is hard to distinguish whether the directions should apply to the outback leg or the return leg. The only solution at present is to edit the route and drag the sections apart very slightly, so that you can select the correct leg (our or back) when adding directions. You can use the Drag Mode to make tweaks to short sections of the route like that.
I've uploaded a route that involves some back-tracking -- coming back in on same road we went out on. When attempting to Add Directions, the directions are automatically given the ending mileage, not the mileage on the way out. In other words, I want to note a turn at Mile 1.0, but Add Direction labels it as Mile 26.0 because we come back that way too. Help!