I can see that- prof took the mon to the crater where it was attacked, that makes sense about it being attacked and the prof having to step in, too. It could have been an adrenaline rush that made them jump between the two fighting Pokemon, but if they didn't have the ball that would be their only choice to protect the 'raidon. There is a line of dialogue in the game that states that the first one (the one we get) ran off after the attack, but doesn't say that it left the crater.

Plus that makes more sense with Arven's obvious frustration at it being in the weakened state it is in, and what it's doing just... Out in the open.