**SPOILERS
Yes, Vader does stab the Apprentice (Galen Marek) when the Emperor first "discovers" him, which is right after Galen reports in on killing Shaak Ti. I heard that in the novel it takes Galen takes 6 months to recover from his injuries, but in the game its a few long cut-scenes in between.
**one ending SPOILER
And the Apprentice can get revenge for that if you play the dark side ending, in which he kills Vader outright. Obviously, that particular ending isn't canon