diff --git a/activitysim/abm/models/util/test/test_vehicle_type_alts.py b/activitysim/abm/models/util/test/test_vehicle_type_alts.py
new file mode 100644
index 000000000..d9cf1c176
--- /dev/null
+++ b/activitysim/abm/models/util/test/test_vehicle_type_alts.py
@@ -0,0 +1,59 @@
+# ActivitySim
+# See full license in LICENSE.txt.
+
+import pandas as pd
+import pandas.testing as pdt
+
+from activitysim.abm.models.vehicle_type_choice import (
+    get_combinatorial_vehicle_alternatives,
+    construct_model_alternatives,
+    VehicleTypeChoiceSettings,
+)
+from activitysim.core import workflow
+
+
+def test_vehicle_type_alts():
+    state = workflow.State.make_default(__file__)
+
+    alts_cats_dict = {
+        "body_type": ["Car", "SUV"],
+        "fuel_type": ["Gas", "BEV"],
+        "age": [1, 2, 3],
+    }
+
+    alts_wide, alts_long = get_combinatorial_vehicle_alternatives(alts_cats_dict)
+
+    # alts are initially constructed combinatorially
+    assert len(alts_long) == 12, "alts_long should have 12 rows"
+    assert len(alts_wide) == 12, "alts_wide should have 12 rows"
+
+    model_settings = VehicleTypeChoiceSettings.model_construct()
+    model_settings.combinatorial_alts = alts_cats_dict
+    model_settings.PROBS_SPEC = None
+    model_settings.WRITE_OUT_ALTS_FILE = False
+
+    # constructing veh type data with missing alts
+    vehicle_type_data = pd.DataFrame(
+        data={
+            "body_type": ["Car", "Car", "Car", "SUV", "SUV"],
+            "fuel_type": ["Gas", "Gas", "BEV", "Gas", "BEV"],
+            "age": ["1", "2", "3", "1", "2"],
+            "dummy_data": [1, 2, 3, 4, 5],
+        },
+        index=[0, 1, 2, 3, 4],
+    )
+
+    alts_wide, alts_long = construct_model_alternatives(
+        state, model_settings, alts_cats_dict, vehicle_type_data
+    )
+
+    # should only have alts left that are in the file
+    assert len(alts_long) == 5, "alts_long should have 5 rows"
+
+    # indexes need to be the same to choices match alts
+    pdt.assert_index_equal(alts_long.index, alts_wide.index)
+
+    # columns need to be in correct order for downstream configs
+    pdt.assert_index_equal(
+        alts_long.columns, pd.Index(["body_type", "age", "fuel_type"])
+    )
diff --git a/activitysim/abm/models/vehicle_type_choice.py b/activitysim/abm/models/vehicle_type_choice.py
index a2ea7b0bd..071061cb8 100644
--- a/activitysim/abm/models/vehicle_type_choice.py
+++ b/activitysim/abm/models/vehicle_type_choice.py
@@ -244,7 +244,19 @@ def construct_model_alternatives(
             ), f"missing vehicle data for alternatives:\n {missing_alts}"
         else:
             # eliminate alternatives if no vehicle type data
+            num_alts_before_filer = len(alts_wide)
             alts_wide = alts_wide[alts_wide._merge != "left_only"]
+            logger.warning(
+                f"Removed {num_alts_before_filer - len(alts_wide)} alternatives not included in input vehicle type data."
+            )
+            # need to also remove any alts from alts_long
+            alts_long.set_index(["body_type", "age", "fuel_type"], inplace=True)
+            alts_long = alts_long[
+                alts_long.index.isin(
+                    alts_wide.set_index(["body_type", "age", "fuel_type"]).index
+                )
+            ].reset_index()
+            alts_long.index = alts_wide.index
         alts_wide.drop(columns="_merge", inplace=True)
 
     # converting age to integer to allow interactions in utilities
@@ -455,11 +467,11 @@ def iterate_vehicle_type_choice(
             alts = (
                 alts_long[alts_long.columns]
                 .apply(lambda row: "_".join(row.values.astype(str)), axis=1)
-                .values
+                .to_dict()
             )
         else:
-            alts = model_spec.columns
-        choices["vehicle_type"] = choices["vehicle_type"].map(dict(enumerate(alts)))
+            alts = enumerate(dict(model_spec.columns))
+        choices["vehicle_type"] = choices["vehicle_type"].map(alts)
 
         # STEP II: append probabilistic vehicle type attributes
         if probs_spec_file is not None: