Hi Fernando,
your detector sensitivity is set to ultra, which might introduce weak points for orientation. I would leave that at the standard setting until you have an extremely difficult model.
You are probably right about the alignment being the cause. You need to inspect the model and try to find misaligned parts. Either use the inspection tool or look for doubled surfaces in the sparce point cloud. If you find them, then you need to improve the alignment until you are satisfied.
Did you try using another distortion model? Brown 4 works best for me - depends on the camera and lens.