Under the 2021 deal, the Justice Department agreed not to prosecute Boeing over allegations it defrauded the Federal Aviation Administration so long as the company overhauled its compliance practices and submitted regular reports. Boeing also agreed to pay $2.5 billion to settle the investigation"
The 2.5 billion sound like a bribe to me, to avoid criminal charges. And Boeing thought that was enough, but it seems they did not assume that the FAA was also serious, that they still need to "overhaul its compliance practices and submitted regular reports".
edit: we are talking about potential manslaughter in hundreds of cases here, because this is what a criminal investigation could lead to, not a fine for violating arbitary regulations