In the first inning of the May 27 Syracuse Nationals - Norfolk Tides game, Syracuse loaded the bases with one out via two singles and a hit-by-pitch. Michael Bowden's 0-2 pitch to Ian Stewart bounced away from catcher Audry Perez. Darin Mastroianni tried to score, but Perez got to the ball quickly and threw to Bowden covering home plate. Bowden tagged Mastroianni before he touched home and Mastroianni was called out. The other runners, Tony Gwynn and Matt Minicozzi, advanced to second and third base, respectively.
How would you score that play? Most fans - even most hardcore baseball fans - would automatically score that play as a wild pitch on which Mastroianni was thrown out. They reason that you have to account for Gwynn and Minicozzi's advance somehow, and that it somehow seems right to charge the pitcher with a wild pitch when he did, in fact, throw a wild pitch.
Those fans are wrong. The correct scoring decision doesn't, to the best of my knowledge, have an official name but it's occasionally referred to as an "Out Advancing" or as a Fielder's Choice. The guiding principle is easily understood - neither a wild pitch nor a passed ball can be charged if a runner is put out without having successfully advanced a base. (The second part of the condition allows a wild pitch to be charged when a runner is thrown out trying to advance a second base - from second to home or from first to third.) Regarding the other runners, they are treated the same way as runners on a double-steal are treated when one of the runners is caught - they are not credited with a stolen base but are considered to have advanced on a fielder's choice.
It's not only fans, but even also the occasional official scorer who doesn't understand this play. A few years ago, there was a similar play at Harbor Park. With runners on first and third, the pitcher's pitched landed in the dirt and bounced a few feet away. The runner on third broke for home, realized that he wasn't going to make it, and tried to return to third. The catcher threw to third in time to retire the runner. While this was going on, the runner on first advanced to second. The game's official scorer insisted that a wild pitch be charged to the pitcher, despite the arguments of myself and the team's media relations director that the scoring rules prohibit it. Eventually, we alerted Major League Baseball Advanced Media that the official scorer wasn't listening to us and that we would have to change the play after he submitted the box score. (MLBAM can unilaterally change official scoring decisions if they contravene the rules or if they are contradicted by facts.)
In fairness to all concerned, the official rule book does not clearly deal with this situation. The rule book is filled with many different scoring rules, principles, and examples, but does not explicitly state the scoring rule or provide an example of this play. A simple declarative subpoint - perhaps something like "Neither a wild pitch nor a passed ball shall be charged if a baserunner is put out without having advanced a base safely." - would clearly instruct the scorer. And, to make it more emphatic, the rule book should include examples of at least three scenarios - a basic wild pitch/passed ball; the out-advancing scenario; the scenario in which a runner is out trying to advance two bases - and the play would be clear.