diff --git a/mace/cli/fine_tuning_select.py b/mace/cli/fine_tuning_select.py
index 19e44d7d..0435e5c3 100644
--- a/mace/cli/fine_tuning_select.py
+++ b/mace/cli/fine_tuning_select.py
@@ -234,17 +234,19 @@ def select_samples(
             ]
         if len(atoms_list_pt_filtered) <= args.num_samples:
             logging.info(
-                "Number of configurations after filtering is less than the number of samples, "
-                "selecting random configurations, for the rest."
+                f"Number of configurations after filtering {len(atoms_list_pt_filtered} "
+                f"is less than the number of samples {args.num_samples}, "
+                "selecting random configurations for the rest."
             )
             atoms_list_pt_minus_filtered = [
                 x for x in atoms_list_pt if x not in atoms_list_pt_filtered
             ]
-            atoms_list_pt_random = np.random.choice(
-                atoms_list_pt_minus_filtered,
+            atoms_list_pt_random_inds = np.random.choice(
+                list(range(len(atoms_list_pt_minus_filtered))),
                 args.num_samples - len(atoms_list_pt_filtered),
-            ).tolist()
-            atoms_list_pt = atoms_list_pt_filtered + atoms_list_pt_random
+                replace=False
+            )
+            atoms_list_pt = atoms_list_pt_filtered + [atoms_list_pt_minus_filtered[ind] for ind in atoms_list_pt_random_inds]
         else:
             atoms_list_pt = atoms_list_pt_filtered