Judges don't like to be made fools of, or used, or asked to take political risks—as doing so can destroy their professional careers. Judge Ellis' anger here is about Judge Ellis—there's no way he believes that Paul Manafort gets to escape prosecution on multiple federal felonies.
2/ The Manafort case is either a career-killer for Ellis, a career-defining case that's not the case he wants to define him, or a case that deeply burdens the rest of his judicial duties due to charges he expects will ultimately be dropped the moment Manafort agrees to cooperate.
3/ If you think Ellis is angry because he thinks there's no case against Manafort; if you think he's angry because he thinks no federal authority—Mueller or otherwise—should prosecute Manafort; if you think Ellis is angry because he believes the feds have lied to him—think again.
4/ I've seen this sort of anger from judges—up close—many times before: if they think the parties before them aren't being blunt about what's "really going on" in the case, they decide they're being played for saps and being put upon and being put in a bad spot and they lash out.
5/ Should the judge have said what he said? No. If the case doesn't go the feds' way, is there a chance these remarks constitute reversible error? Yes. But the Occam's Razor explanation here is that you have a judge blowing off steam and hoping neither party asks for his recusal.
