diff --git a/medcat-v2/medcat/components/addons/meta_cat/data_utils.py b/medcat-v2/medcat/components/addons/meta_cat/data_utils.py
index caf568b9f..3c14982e5 100644
--- a/medcat-v2/medcat/components/addons/meta_cat/data_utils.py
+++ b/medcat-v2/medcat/components/addons/meta_cat/data_utils.py
@@ -126,6 +126,10 @@ def _prepare_from_json_loop(document: dict,
                         else:
                             ctoken_idx.append(ind)
 
+                if not ctoken_idx:
+                    # Entity span did not map to any tokens
+                    continue
+
                 _start = max(0, ctoken_idx[0] - cntx_left)
                 _end = min(len(doc_text['input_ids']),
                            ctoken_idx[-1] + 1 + cntx_right)
diff --git a/medcat-v2/medcat/components/addons/meta_cat/meta_cat.py b/medcat-v2/medcat/components/addons/meta_cat/meta_cat.py
index 5386a8dc1..05fb4a185 100644
--- a/medcat-v2/medcat/components/addons/meta_cat/meta_cat.py
+++ b/medcat-v2/medcat/components/addons/meta_cat/meta_cat.py
@@ -736,6 +736,10 @@ def prepare_document(self, doc: MutableDocument, input_ids: list,
 
             # Start where the last ent was found, cannot be before it as we've
             # sorted
+            if not ctoken_idx:
+                # Entity span did not map to any tokens (e.g. entity at
+                # document boundary or beyond tokenised text length)
+                continue
             last_ind += ind  # If we did not start from 0 in the for loop
 
             _start = max(0, ctoken_idx[0] - cntx_left)
@@ -825,6 +829,9 @@ def _set_meta_anns(self,
         ents = self.get_ents(doc)
 
         for ent in ents:
+            if ent.id not in ent_id2ind:
+                # Entity was skipped in prepare_document (no token mapping)
+                continue
             ent_ind = ent_id2ind[ent.id]
             value = id2category_value[predictions[ent_ind]]
             confidence = confidences[ent_ind]
diff --git a/medcat-v2/medcat/trainer.py b/medcat-v2/medcat/trainer.py
index 7a2b32ef8..d8f4b5f80 100644
--- a/medcat-v2/medcat/trainer.py
+++ b/medcat-v2/medcat/trainer.py
@@ -336,8 +336,15 @@ def _train_meta_cat(self, addon: AddonComponent,
         cat_name = cnf.general.get_applicable_category_name(ann_names)
         if cat_name in ann_names:
             logger.debug("Training MetaCAT %s", cnf.general.category_name)
+            # Provide a save directory for auto_save_model support —
+            # train_raw requires save_dir_path when auto_save_model is True
+            save_dir = None
+            if cnf.train.auto_save_model:
+                import tempfile
+                save_dir = tempfile.mkdtemp(
+                    prefix=f"metacat_{cnf.general.category_name}_")
             # NOTE: this is a mypy quirk - the types are compatible
-            addon.mc.train_raw(cast(dict, data))
+            addon.mc.train_raw(cast(dict, data), save_dir_path=save_dir)
 
     def _train_addons(self, data: MedCATTrainerExport):
         logger.info("Training addons within train_supervised_raw")