The problem is related to the `use_index_order` option of `BLI_kdtree_3d_calc_duplicates_fast`. With this option, the higher index is expected to be less than `tree->nodes_len`.
The problem is related to the `use_index_order` option of `BLI_kdtree_3d_calc_duplicates_fast`. With this option, the higher index is expected to be less than `tree->nodes_len`.