How many points are you left with during the pointcloud conversion? (ALPACA should report the number of points). If it is too few, that might be the problem.
Try changing both alpha and beta values together. Increasing CPD iterations will probably be useful as well.
Finally, the current ALPACA module will be deprecated soon, and we will switch to an ITK based implementation (instead of open3d we are currently using). Make sure you start using, it is already available with SlicerMorph (it is called ALPACA-preview), but it is hidden.
Go to Application Setting->Developer->Enable developer mode.
then, open the module finder, and check Testing.
