Most errors I have seen usually relate to the inconsistencies between the 1:25K and the 1:100K maps. Most 100K maps use metric, and often the conversions can be many dozens of feet awry, when compared to the 25K maps.
Consider that most 25K topo maps were mapped back in the 40s and 50s, and sporadically updated, it's no surprise there are errors and missing canyons, etc. I hope the USGS plans to update all its 25K maps in the near future, using more advanced technology. There's no reason large land forms have to be ignored. Fly a plane over it, shoot some photos, beam some sonar and lasers, and be done with it. It would be nice to have more spot elevations available, for instance. Nevertheless, despite the occasional blunders, the original feat of mapping the entire US is still a very impressive one. We just need to do it again; it's about that time.