The one I still remember was with Semien - he was treated as a utility guy early, but he was playing SS more than any other position on the way up through the minors. When he got sent to the As, he was terrible defensively at first, but when they had Washington start working with him there was an article in the local Oakland papers about how Semien had never done the basic fielding drills that everyone is supposed to do at SS. This wasn't them taking a shot at the White Sox, this was a positive article about how they expected him to get better once he got to do the basic work, and turns out the article was correct.
But, from a White Sox perspective, this was an indictment I never forgot. How on earth does a guy come up through your system, get labeled as a utility guy, but also spend most of his time at SS, and yet not go through basic SS fielding and positioning drills? Where did they expect him to get to practice these things, did they expect him to Google all of them and do them on his own? They had him for years and this was the case.
I don't find it that surprising that so many guys come up with the White Sox and struggle, and I don't think it's scouting as much as it is a complete lack of practice and no interest in practicing. Guys in the minor leagues are supposed to teach themselves, that's the way it's' done here.