diff --git a/sqlmesh/core/plan/stages.py b/sqlmesh/core/plan/stages.py
index b50edfbb01..863e53387f 100644
--- a/sqlmesh/core/plan/stages.py
+++ b/sqlmesh/core/plan/stages.py
@@ -431,7 +431,11 @@ def _get_physical_layer_update_stage(
         return PhysicalLayerUpdateStage(
             snapshots=self._get_snapshots_to_create(plan, snapshots),
             all_snapshots=snapshots,
-            snapshots_with_missing_intervals={s.snapshot_id for s in snapshots_to_intervals},
+            snapshots_with_missing_intervals={
+                s.snapshot_id
+                for s in snapshots_to_intervals
+                if plan.is_selected_for_backfill(s.name)
+            },
             deployability_index=deployability_index,
         )
 
diff --git a/tests/core/test_plan_stages.py b/tests/core/test_plan_stages.py
index c8989f9e83..b806b95b75 100644
--- a/tests/core/test_plan_stages.py
+++ b/tests/core/test_plan_stages.py
@@ -141,6 +141,10 @@ def test_build_plan_stages_basic(
         snapshot_a.snapshot_id,
         snapshot_b.snapshot_id,
     }
+    assert {s.snapshot_id for s in physical_stage.snapshots_with_missing_intervals} == {
+        snapshot_a.snapshot_id,
+        snapshot_b.snapshot_id,
+    }
     assert physical_stage.deployability_index == DeployabilityIndex.all_deployable()
 
     # Verify BackfillStage
@@ -357,6 +361,7 @@ def test_build_plan_stages_select_models(
     assert len(physical_stage.snapshots) == 1
     assert {s.snapshot_id for s in physical_stage.snapshots} == {snapshot_a.snapshot_id}
     assert physical_stage.deployability_index == DeployabilityIndex.all_deployable()
+    assert physical_stage.snapshots_with_missing_intervals == {snapshot_a.snapshot_id}
 
     # Verify BackfillStage
     backfill_stage = stages[2]