As an assistant coach and team scorer for my son’s 11U Cal Ripken Tournament Team, I stumbled into some interesting issues around the scoring of errors. I recently did a great deal of research to try and make sure I was scoring correctly. Scoring errors has a subjective component so there is is really no such thing as scoring correctly but I wanted to be as accurate as is possible and I wanted to make sure I was scoring according the actual rules and guidelines rather than my own personal notion of what a baseball error is.
The main sources of controversy I ran into were: 1) if a ball that drops in in the outfield can be an error and 2) if every ball that is handled with problems is automatically an error in the infield.
For both questions, it is helpful to know about the baseball concept of ordinary effort.
In 2007, the notion of ordinary effort was specifically defined in the MLB rules. 
Ordinary effort refers to the effort that a fielder of average skill at a specific position should exhibit on a play, with due consideration given to the conditions of the playing field and the weather. Umpires must use that standard when calling infield fly plays, and the official scorer uses it to judge what constitutes an error, a wild pitch, a passed ball and a sacrifice. 
Let’s get back to the first question of if the scorer can give an error if an outfield fly ball is not handled and it appears that the fielder could have gotten the ball. The answer is yes according to the MLB rules for errors and the MLB definition for ordinary effort above.
It is not necessary that the fielder touch the ball to be charged with an error. If a ground ball goes through a fielder’s legs or a fly ball falls untouched and, in the scorer’s judgment, the fielder could have handled the ball with ordinary effort, the official scorer shall charge such fielder with an error.
So we can see that a ball that does not touch a glove can still be considered an error, specifically an outfielder that could have caught a fly ball with ordinary effort – that is if an average fielder at that level considering the weather and field conditions – should be scored as an error. I did not score these as errors very often because it is pretty common for outfielders to play it safe to some extent at 11U but did charge a few when, it my judgement, it was clear that the ball could have been caught with ordinary effort. I don’t think this comes up very often in Major League Baseball because it just does not happen often. [There was a controversy about it when it was charged in one case and it was appealed by David Ortiz and was overturned.  However, I would say in this case the MLB ignored their own rule book.] So I suspect there can be a mistaken belief that only a mishandled (dropped or bobbled) ball that comes into contact with the glove can be error but that is not what the MLB rules say. Another clear counterexample of this is a ball that goes under an infielder’s legs which I would almost always consider an error with the exception of a very bad hop.
In the above case, I got pushback for charging an error.
I also got some pushback from not charging errors for balls that did come into contact with a glove. Again, there seems to be a belief that a ball that comes into contact with the glove and is problematic for the fielder has to have an error charged. This also is not right. The scorer has to judge whether the ball was playable with ordinary effort. In our last game of the season, another coach thought my son should have charged with an error. He made a dive for a hard-hit ground ball at shortstop. He stopped the ball but did not quite come up with it in time for a throw. It was a ball that an average infielder at his level would not have made, that is, not playable with ordinary effort so I did not charge an error. Of course, it’s easy be a parent in cases like this and give your own kid more leeway but I believe would make the same call for any diving (or leaping) catch and that seems to be where most scorers draw the line.
I think the difficulty is being consistent. There is a tendency to give defense some leeway especially at this level but that makes it harder to be consistent in my experience. Note that the official MLB rules actually say to favor the hitter when in doubt.
Rule 9.05(a) Comment: In applying Rule 9.05(a), the official scorer shall always give the batter the benefit of the doubt. A safe course for the official scorer to follow is to score a hit when exceptionally good fielding of a ball fails to result in a putout.
Some scorers give a lot of leeway with hard hit ground balls but what constitutes a hard-hit ground ball exactly? This wording in the MLB rules seems to allow some judgment for scoring a hit for a hard hit (or very slow) ground ball.
The batter reaches first base safely on a fair ball hit with such force, or so slowly, that any fielder attempting to make a play with the ball has no opportunity to do so.
Once again, there are some grey areas that make the judging of errors subjective.
The rule about considering ordinary effort is a good one and encourages players to go for great plays rather than playing it safe and I believe that is why it was put in place – though I could not find the specific history of the concept of ordinary effort.
The whole notion of evaluating kids especially on fielding percentage (putouts/chances) is suspect anyway for a number of reasons and parents, coaches, and kids should not get worked up about it in my view. For one, different positions have different levels of difficulty with shortstops specifically and third basemen to a lesser extent having higher error rates due to the difficulty of their positions.  Also, fielders who are quicker or more aggressive – both good things – are going to have more chances to make errors. Lastly, the subjective nature of scoring errors is going to make comparing and judging these numbers challenging.
In scoring youth baseball, we need to think about what the statistics are for. It is going to be problematic if we are using them to evaluate kids and share this with parents (beyond their own kid’s stats). If we are using them to inform our decisions as coaches and we can take off our parent hats and think solely as coaches, that can work. For example, we might look at on base percentages (OBP) when we make up our batting order. Personally, I like to share good stats with kids during and after the season is over to highlight things they did well. But we need to realize that there is a subjective aspect to scoring, especially errors, and that scorekeepers, as long as they do understand the definition of errors and ordinary effort are doing their best to score accurately in order to help the kids and the team. There also needs to be a realization that scorekeeping is hard, especially when there are lots of substitutions to contend with or when there is a lot going on in big plays.