None of the articles I found said anything other than the fact that Badger was found guilty of negligence. None of them said exactly what they did or didn't do that caused them to be found negligent.
And I couldn't read the article you linked because it kept scrolling down to an infographic and wouldn't let me read the article from the beginning. That's why I'm really starting to get aggravated with the insistence on "media content rich" webpages, they put so much extra crap on them that you can't find what you're looking for.
If you just keep scrolling it gets to the article, I agree it's annoying as $##%. However if you search for atf violations there are a whole host of local article's based on the same research.
For the badger guns saga you'll need a Milwaukee journal sentinel login to get to the archives.
In short, they were the go to place for criminals to acquire guns. Every time they were inspected by federal, state, or local entities violations were found. It was recommended that their license be revoked in 2006 - they "changed ownership" and continued business as usual. In 2009 or 2010 they were specifically listed as one of the ten largest sources of crime guns in Chicago with (I think) the shortest time between sale and crime. What they were doing was illegal, but when caught committing crimes they faced no comeuppance at all.