"it will happen tonight ... Tonight, before midnight, the servant will break free and set out to rejoin his master."

that still fits with the timeline. We dont specifically know when Barty Crouch Jr escaped from his fathers house... the first time we see him is at the start of GoF at the riddle house with Voldemort, which would imply he didnt just turn up that moment... for all we know he could have escaped and met up with Voldemort the same night that Pettigrew did.

Remember, there were two possibilities with the Harry Voldemort prophecy too... its possible that it could have applied to Neville too, but Voldemorts choice marked Harry as the chosen one.