Some evidence suggests that Bill James is all over this.
Baseball is a quick game, and umpires sometimes miss calls. They call 'em as they see 'em, but sometimes they don't see 'em. So when, for example, a first-baseman grabs a ball thrown off the basepath by the second baseman, tags the batter-runner on the first base line before he, the batter-runner, touches the bag, but neither the home plate umpire nor the first base umpire sees this. The official scorer usually assigns an error to the second baseman or (rarely) the first baseman. Why? If replays show he would have gotten the out, then it needs to be called something else. An example might be drawn from a strikeout where the catcher drops or misses the pitch, and the batter-runner moves to first base. The pitcher still gets the strikeout but no out gets counted. Maybe the second baseman gets the putout i.e. it does not affect his fielding percentage but the batter-runner doesn't get a hit. Reached Base on Umpire's Missed Call? Not sure how the umpire feels about, but the fielders sure know how they feel about it, and will let everybody in the stadium know.