I think you're being a little consciously naive.

Choosing not to prosecute (especially because prosecuting tax fraud requires proof of willfulness) and simply collecting a tax deficit is pretty common, especially in cases of corporate tax evasion.

The disagreement in this case is called a tax deficit, and is what I meant by wrong. It's also the first necessary part of tax fraud.

EDIT: Also, if you read about the source of the $345 million tax bill (from the article), it's hard to see how this would've been a problem with "unclear phrasing"...