It's not a mistake, these list weights aren't just made up out of thin air. Even when they're way off, there's a reason, and that reason is usually that they're very, very outdated. That's the case with Wilfork: he's listed at 323 because that's what he weighed at the combine over a decade ago, back when he was coming out of Miami as a big-bodied DT who was nevertheless adept at crashing into the backfield and making plays behind the line. He was also known for having issues with weight control even then. So, given that he was drafted onto a team that expected him to be a two-gapping NT, it made sense for him to gain weight. And gain weight he did, all while his combine weight stayed his 'official' weight.
Jones is a case where his weight has been updated over the past five years since the combine. That's part of the solution to the problem you're highlighting, not part of the problem itself.