With trails such as the PCT you'll often find 2 routes, one is a stock route and one is a hiker route. Many times the stock route is the "official" route. I suspect that may be the case with the Mist Trail, though I'm not sure.
Like Silver Lake, you'll probably find a few spots have been rerouted for the purpose of rehabilitation.
Mist trail is not part of the JMT, but below the bridge the JMT runs on the north side of the river. Above the bridge, the JMT follows the horse trail to the top of the falls (and more asphalt!). Mist trail is something a lot of people choose as an alternative, because it has some highlights worth the steep steps, but I bet many southbound Day 1 hikers still choose the regular route for its easier grade.
Evolution Lake has been re-routed quite a few years ago and nobody does take the old route any longer. The Silver Lake route also has been east of the lake for well over a decade. In fact, I think even in 1988 on my first trip, we were east of the lake.
Two summers ago they re-routed a part of the Forester Pass north ramp at the highest meadow, but only for about a quarter mile.
Looking at a few of my GPS tracks, I can see deviation from the USGS map route very frequently, and none of those deviations are reception errors. The trail has either been re-routed in a lot of areas since teh USGS maps were made, or, more likely, the map makers were sloppy. Just look at the track below - other than the ridge detour skipping final switchbacks north of Forester Pass where there was just a ton of snow, we were right on the trail all day. I'd say 30% of the map for that day between our camp north of Forester and Guitar lake is wrong. I know from the terrain features on the map that the GPS track very much represents where we hiked.
Forester to Guitar Lake 
