Between his drug addiction and traumatic past, Justin is a loose cannon throughout pretty much every season. With the help of Clay and his family, he's able to recover (at least somewhat), and in the season two finale it seems like his romance with Jessica might be back on (reminder: she cheats on Alex with Justin the night of the dance, leaving a mark). When you take all this into account — his addiction, his unstable mental state, his love for Jess — and combine it with the fact that he hates Bryce, the odds of Justin killing him start to look pretty strong.
This dynamic is explored in season three, particularly if Justin actually does hate his former friend or not. After learning of his death, he breaks down on the football field, telling Clay that Bryce was the first person to "give a sh*t about" him, and through it all he was basically his brother. Was that Justin's guilt shining through? Nope. Justin did not kill Bryce, but he was at the waterfront of the time of his death covertly buying drugs from a dealer named Halls.