Well, first of all, there's no such thing as a plot hole in fiction. Anything that happens in fiction, happens the way it does because the author (content creator) SAYS it happens that way. If I've written a book in which the sun rises in the east and sets in the west, and then write a discription later that has the opposite happening on a single day... AND never bother to explain that inconsistancy... that isn't a "plot hole." I just either a: deemed it not important enough to waste words on, b: plan to explain it later, or c: I'm leaving it as a dangling thread to fuck with nitpickers because it makes me laugh.
That being said, the Willhelm thing bothered me too. It wasn't a so-called "plot hole" (it couldn't be, they don't exist in fiction) it was just this... The most well written, most highly characterized, most interesting character in the series to this point... was a complete moron.
I mean bad, sub bond-villain wannabe level of antagionist. Why allow the vault hunters access to the one thing that assures them victory, and not give the same to your own dudes. Namely the new-u system. Clearly (because of the events of BL 2) he has complete access to it. So unless his plan is for the vault hunters to win and eventually kill him and take over Pandora, its vaults, and all hyperion's holdings on it... he's just a moron.
I could think of a dozen ways he could have tricked the new vault hunters into using the power core without having to sacrifice Willhelm... The first one came to me after about 5 seconds. As fun and interesting a bad guy as Jack is to square off against... BRICK is a better and more strategic thinker than Jack is.