All of the above. Mostly too aggressive and swinging at pitches where it's hard to make good contact, Williams doesn't take a lot of strikes early in counts (Altherr does), which he should learn to do, especially the first time he sees a pitcher (so you can see his release point and motion and have a better chance of picking up the pitch out of his hand).
With less than two strikes, young hitters have to learn you don't want to swing at a pitch that's not in your "kill zone." Even if you hit it, you're likely to make an out (poor contact, low exit velocity). BABIP tends to reflect, speed, exit velocity and luck, over larger samples the luck fltters out.
This is why this team is frustrating to watch right now (and probably drives Stairs crazy at times). Young hitters want to hit, and have to learn to "work" an AB to get a pitch they can handle. Watching Herrera trying to hit a low slider is cringe worthy - he often decides to hit when the ball is leaving the pitcher's hand before he has a chance to recognize the pitch. This is why Stairs is reworking swings and trying to get hitters to keep their hands back, buy that extra tenth of a second to recognize the spin on a pitch.
A good way to see the difference is to watch the Phillies hitters and contrast them with good hitters on other teams, and how they handle ABs. Phllips for example, is a great technical hitter, tries to pound the ball with less than two strikes, then protects the plate and fouls off pitches he can't handle until he can make good contract or draw a walk. The Nats do a great job of laying off close balls, forcing pitchers to throw it in the K-zone. Getting ahead in the count gives a hitter a huge edge.
The Philiies have one of the highest rates of pitches per PA, evidence that Stairs is having an impact. I think it's just a matter of time, kids who've swung their way up the organizational ladder aren't going to become polished ML hitters overnight. But it's a matter of percentages, reduce the percentage of bad pitches you swing at, increase the percentage of PAs where you "barrel" at least one pitch, and you'll be a better hitter. You're still going to get fooled or be beat by strikes you can't handle, but you won't be beating yourself.