diff --git a/flaml/automl/automl.py b/flaml/automl/automl.py
index 74b8741ac0..3d9e09b62f 100644
--- a/flaml/automl/automl.py
+++ b/flaml/automl/automl.py
@@ -2724,6 +2724,58 @@ def cv_score_agg_func(val_loss_folds, log_metrics_folds):
         )
         self._auto_augment = auto_augment
 
+        if "auto" == estimator_list:
+            if self._state.task == "rank":
+                estimator_list = ["lgbm", "xgboost", "xgb_limitdepth"]
+            elif _is_nlp_task(self._state.task):
+                estimator_list = ["transformer"]
+            elif self._state.task == TS_FORECASTPANEL:
+                estimator_list = ["tft"]
+            else:
+                try:
+                    import catboost
+
+                    estimator_list = [
+                        "lgbm",
+                        "rf",
+                        "catboost",
+                        "xgboost",
+                        "extra_tree",
+                        "xgb_limitdepth",
+                    ]
+                except ImportError:
+                    estimator_list = [
+                        "lgbm",
+                        "rf",
+                        "xgboost",
+                        "extra_tree",
+                        "xgb_limitdepth",
+                    ]
+                if self._state.task in TS_FORECAST:
+                    # catboost is removed because it has a `name` parameter, making it incompatible with hcrystalball
+                    if "catboost" in estimator_list:
+                        estimator_list.remove("catboost")
+                    if self._state.task in TS_FORECASTREGRESSION:
+                        try:
+                            import prophet
+
+                            estimator_list += ["prophet", "arima", "sarimax"]
+                        except ImportError:
+                            estimator_list += ["arima", "sarimax"]
+                elif "regression" != self._state.task:
+                    estimator_list += ["lrl1"]
+
+        if isinstance(starting_points, dict):
+            _estimators_from_starting_points = starting_points.keys()
+            if not any(i in estimator_list for i in _estimators_from_starting_points):
+                logger.warning(
+                    "The proivded starting_points {} is removed as it does not contain relevant estimators as keys"
+                    " and is thus NOT used. Please check the required format of starting_points.".format(
+                        starting_points
+                    )
+                )
+                starting_points = {}
+
         _sample_size_from_starting_points = {}
         if isinstance(starting_points, dict):
             for _estimator, _point_per_estimator in starting_points.items():
@@ -2843,46 +2895,6 @@ def is_to_reverse_metric(metric, task):
             error_metric = "customized metric"
         logger.info(f"Minimizing error metric: {error_metric}")
 
-        if "auto" == estimator_list:
-            if self._state.task == "rank":
-                estimator_list = ["lgbm", "xgboost", "xgb_limitdepth"]
-            elif _is_nlp_task(self._state.task):
-                estimator_list = ["transformer"]
-            elif self._state.task == TS_FORECASTPANEL:
-                estimator_list = ["tft"]
-            else:
-                try:
-                    import catboost
-
-                    estimator_list = [
-                        "lgbm",
-                        "rf",
-                        "catboost",
-                        "xgboost",
-                        "extra_tree",
-                        "xgb_limitdepth",
-                    ]
-                except ImportError:
-                    estimator_list = [
-                        "lgbm",
-                        "rf",
-                        "xgboost",
-                        "extra_tree",
-                        "xgb_limitdepth",
-                    ]
-                if self._state.task in TS_FORECAST:
-                    # catboost is removed because it has a `name` parameter, making it incompatible with hcrystalball
-                    if "catboost" in estimator_list:
-                        estimator_list.remove("catboost")
-                    if self._state.task in TS_FORECASTREGRESSION:
-                        try:
-                            import prophet
-
-                            estimator_list += ["prophet", "arima", "sarimax"]
-                        except ImportError:
-                            estimator_list += ["arima", "sarimax"]
-                elif "regression" != self._state.task:
-                    estimator_list += ["lrl1"]
         # When no search budget is specified
         if no_budget:
             max_iter = len(estimator_list)
@@ -3557,6 +3569,25 @@ def _search_sequential(self):
                     state.best_config,
                     self.data_size_full,
                 )
+                if getattr(self._trained_estimator, "params", {}) and getattr(
+                    self._trained_estimator, "ITER_HP", None
+                ):
+                    _hp_trained_iter = self._trained_estimator.params.get(
+                        self._trained_estimator.ITER_HP
+                    )
+                    _best_config_iter = self.best_config.get(
+                        self._trained_estimator.ITER_HP
+                    )
+                    if _hp_trained_iter != _best_config_iter:
+                        logger.warning(
+                            "Early stopping happened when retraining a model with the best configuration."
+                            f" The best config's {self._trained_estimator.ITER_HP} is {_best_config_iter}"
+                            f" and the actual {self._trained_estimator.ITER_HP} used for retraining the model is {_hp_trained_iter}."
+                            " This early stopping happens because flaml needs to do its best effort to"
+                            " retrain without violating the time budget when retrain_full is set to 'budget'. "
+                            " If this mismatch is not desired, please set retrain_full to True."
+                        )
+
                 logger.info(
                     "retrain {} for {:.1f}s".format(self._best_estimator, retrain_time)
                 )
diff --git a/test/automl/test_warmstart.py b/test/automl/test_warmstart.py
index 74cf8c37f2..8aaedb0289 100644
--- a/test/automl/test_warmstart.py
+++ b/test/automl/test_warmstart.py
@@ -219,6 +219,15 @@ def test_FLAML_sample_size_in_starting_points(self):
         except AssertionError:
             pass
 
-
+        # In the following test case, the starting_points is not provided in the
+        # right format and thus we expect a warning for removing the provided
+        # starting_points when the fit function is called
+        automl5 = AutoML()
+        automl_settings["starting_points"] = automl3.best_config
+        automl5.fit(
+            X_train,
+            y_train,
+            **automl_settings,
+        )
 if __name__ == "__main__":
     unittest.main()