He no doubt wants to know why Ten kissed Madame de Pompadour and left Rose alone in the spaceship with evil robots and....heaven forbid, Rickey, (He's rather mad about this, as he's very protective of Rose. He's sure that Ten could've brought Rose along instead of just leaving her there with Rickey the Idiot.) He's also annoyed with Eleven, who he's sure is an imposter and is definitely not him, (Nine does not and never will think fezzes, or bowties, are cool), and he also wants to know, WHO ON EARTH IS RIVER?!
So yes, Nine is angry at them both and wants a DNA test to see if they're actually him or not, because until he has proof, Nine will not believe it.