I think we break things down pretty well and give the "little things" as much attention as reasonably possible. We figure out in the winter what kind of squad we have coming in and what they will need the most work on. Of course the big things require the bulk of practice time... fielding, throwing, hitting, pitching, positional responsibilities, etc. There are things that must be done daily or nearly every day. There are lots of limitations to factor in.... one field, small roster, players that play multiple positions, etc. So, for example, it is always tough to allocate adequate time for catcher drills when the field is needed for other infield work (and so are the other catchers). The pitchers are, for the most part, also the fielders so when we do bullpens (which we schedule regularly) it disrupts other defensive drills. All this said, we try to plan on also covering all the "little things" at least a couple times prior to first game and then touch on them at least on occasion.
But, here's an example of what happens...
We covered the responsibility and specific read and mechanics of the R1 for a hit and run in depth prior to season and early in season. We reinforce with some versions of our batting practice routines. We haven't had occasion to use it much recently. So, the other day, we ran a different batting practice routine that put more spotlight on the R1 breaking on the hit and run. MOST of the players had COMPLETELY forgotten what they had been drilled on so extensively earlier in the season. This happens more than you would think. We spend part of every day working on bunt execution in the cage and on the field. It is often worked on in live situations. Our players get thousands and thousands of bunt reps with very specific instruction and coaching. All three coaches that help teach this skill are college level guys who could still execute bunts at a 90+ % success rate in a BP setting. Yet, still, there are days where our players can't get a bunt down against straight BP pitching to save their lives. It's mind boggling. We constantly find ourselves saying "we just covered that" or "we just worked on that" when a player looks clueless with a "little thing" situation or execution opportunity.
So, it's not always because it doesn't get worked on or the coaches are idiots.
By the way, Iowamom, be careful. There are plenty of situations when you do want to throw down to second with runners on 1st & 3rd with two outs. And even if you don't, you sure don't want to broadcast what you are going to do by not having the MIF cover the bag. That coach may have been as inept as you say but based on the info given, it is also possible that your 14 y.o. could have learned something.