Dear @Jason.Jonkman,
Thank you for your reply. That helps a lot since we also have seen the similar long structures in our LES precusor simulations using amr-wind. I have tried to increse the domain up to 40D (diameter of rotor), but still cannot break these structures, it might need to increase further the size of domain. I will try to rotate the mean wind direction.
Similar discussion can be found in the forum SOWFA Support - Wind & Water / Computer-Aided Engineering Software Tools - NREL Forum for those are interested.
Best regards.