WTF does that mean?
Call me crazy, but I would've thought the "rules" would be the laws on the books in this regard. Then again, I didn't go to law school, so what do I know...
The judge's rules are the rules of the court, the government violated the court's rules. "Her" rule was based on legal principles which govern the case, she did not make them up.
The judge makes the decision to have witnesses sequestered (usually based on a request from either the prosecutor or the defense). The judge (referred to as "the court") makes the rules, but this rule is not uncommon and has been the case in most trials.