If the scene uses a default rifle, they will use their Assault Rifle, Sniper Rifle or Shotgun, in that order of preference. If they have neither they will use the default pistol.
If the scene uses a default pistol, then Shepard and the squad will use a Heavy Pistol if they are carrying one, if not they will use their SMG. If the scene is animated to use a certain type weapons then it will use the custom weapons as the animator has designed. A simple code fix to make sure that Shepard and the Squad use their carried pistol or rifle (if available) instead of the default Avenger or Predator.
