There is a spot on the Thoreau Falls Trail (heading N along the river) where the trail enters a large open section. The first time I skied the lollipop route (2002), I wasted some time looking for the trail before I realized that the trail would be easy to find on the far side due to terrain restrictions. On the 2011 repeat with Becca, I recognized the spot and we headed directly over to the far side. (There were no tracks to follow either time. And, of course, one cannot always tell if the tracks go where one wants...)
There was another spot on the Shoal Pond Trail where the trail appeared to go through a large open area. After scratching our heads for a bit, we consulted the GPS (with the WMNF tracks installed) which said that it was below a cliff off to the side. We looked and could see a faint corridor down below. There was no clue as to where the trail dropped down and it took us quite a while to find a route. Without the GPS, we probably would have had to turn back. (I have talked to someone else about this spot--he got "confused" too...)
You don't need to be on the trail all the time--you just need to know that you can find it (and get to it) when you need it.
Doug