12:24 p.m. on July 6, 2009 (EDT)
You have encountered a standard property of maps - inaccuracy and incompleteness. Basically, you just have to build your map and navigation skills and deal with it (you could have taken my "Finding Your Way" land navigation workshop at the end of last month and gotten instruction and hands-on experience ;) )
This is something that people who have less than a couple dozen hikes and less than 4 or 5 years regular hiking experience discover to their dismay, and sometimes discover the hard way by getting thoroughly lost.
Basic fact - there is no such thing as a complete, thoroughly up to date, fully detailed map. Even satellite and aerial photos go out of date quickly and in snow areas are incomplete seasonally. The most complete and accurate maps in the world, the USGS topographic 7.5' quads, have lots of errors and omissions, and in some cases are sadly out of date.
There are several reasons for this. First and most obvious is that things change - trails are abandoned, new trails are built, game trails become more prominent, "social" trails are built up over time (especially by mountain bikers who decide to go off-trail, but also by hikers taking "shortcuts" and "herb farmers" going to their concealed "farms"). In winter, snow covers trails, and with seasonal vegetation changes, trails are concealed, then revealed.
A second reason is that features are included or omitted according to the purpose of the map, something you discovered. An equestrian map will show permitted or recommended horse trails, a mountain biking map will show trails open to mountain bikes (and in ski resorts that have summer mountain biking programs, will show the ski runs and cat tracks that are open to bikers), hiking trails will show the authorized hiking trails (and often omit maintenance roads, which don't always have signs saying "maintenance road, do not enter"), and nature and historical trails will show only the trail of interest (with the important signs and points to be explained marked).
A third, and very important, reason is that you cannot put every single detail on the map sheet, because trying to do so would clutter the map to illegibility. So the map will be "simplified". Even orienteering maps, which include the more prominent boulders, rocky ground, fallen logs, "root stocks", stumps, and shallow reentrants (a "reentrant" is basically a gully, with some being barely noticeable to the inexperienced), omit a lot of fine detail.
Something that adds to the confusion for the less experienced is that a lot of maps, especially the "free" handout maps, are over-simplified, with the difficulty of interpretation being exacerbated by being variable scale from one part of the map to another.
A basic skill that comes only with experience (sometimes experience in the particular part of the country or even the particular hiking area) is recognizing when that trace is the main hiking trail, a game trail that is heavily used ("game trail" includes livestock trails in some areas where grazing is allowed), a "social" trail, or an abandoned trail (some "abandoned" trails are in better condition than the trail that replaced them). In some areas which have hardy grasses and/or lots of rain, the "main" trail can appear to just be a grassy area (a recent episode of "Expedition Africa" showed the group getting confused in just such an area). There is a marked trail in the Big Sur area that gets overgrown during every winter rainy season with the bushes (mostly manzanita and coyote brush, but a lot of poison oak as well) to the point that the official trail is difficult to recognize if you don't know what to look for, but the game trails that crisscross the area look like the official trail.
The skill you want to develop is mostly recognizing what the trail you want looks like and differentiating it from game trails. Part of this is the configuration of the trail and "staying in touch with the map". This means keeping track of the wiggles in the trail, stream crossings, distance you have traveled (maybe using pace counting), surrounding landmarks, and so on. If the map is not to scale or is some sort of "perspective view" chart (as ski resort maps often are), this gets a bit challenging.
But do keep in mind that maps are always inaccurate, incomplete, and out of date (even with satellite and aerial photography, the USGS requires a couple decades to update its excellent topographic maps). Sometimes using satellite and aerial photos (e.g., Google) helps, but photo-interpretation is a skill that demands a lot of training to do properly, especially in heavily vegetated areas (around here, it is hard to see even paved roads under the heavy redwood canopy that covers the Santa Cruz Mountains in aerial and satellite photos). Work on your skills in navigating without aid of maps, compass, and electronic widgets.
Takes practice, but it is doable, and most of all, it is a lot of fun!