True, and it's the rather odious practice of civil forfiture where the goods themselves are "charged".
However there also seems to be some potential that the complaint that the ATF was being "confusing" just means a factor of Cav Arms wanting to hear what they wanted to. Even when you take a huge grain of salt, or distrust the ATF and fed.gov completely, there are a lot of pretty easily verifiable material facts that the complaint alleges that look very bad for Cav Arms.
I have ZERO love for the ATF, but if even one of the allegations was true, then these guys were major screwups.
For all I know the plea deal was a gift, because the prosecutor believes they really aren't "gun-runners", just incapable of following directions and maintaining records.