diff --git a/src/control/repos/indexer.rs b/src/control/repos/indexer.rs
--- a/src/control/repos/indexer.rs
+++ b/src/control/repos/indexer.rs
@@ -479,6 +479,9 @@
         &self,
     ) -> Result<Option<impl futures::Stream<Item = std::io::Result<bytes::Bytes>> + Send + 'static>>
     {
+        if self.state.ephemeral {
+            miette::bail!("CAR generation is not supported in ephemeral mode");
+        }
         if !self.state.stores_record_bodies() {
             miette::bail!("block storage is not available in this mode");
         }
@@ -547,11 +550,10 @@
         // sanity check: rebuilt root should match stored commit data in full-index mode
         let computed_root = mst.get_pointer().await.into_diagnostic()?;
         if computed_root != atp_commit.data {
-            tracing::warn!(
-                computed = %computed_root,
-                stored = %atp_commit.data,
-                did = %self.did,
-                "mst root mismatch (expected in filter mode)",
+            miette::bail!(
+                "mst root mismatch for {}: computed {computed_root} != stored {}",
+                self.did,
+                atp_commit.data,
             );
         }
         store
@@ -667,4 +669,63 @@
         Ok(())
     }
 
+
+    #[tokio::test]
+    #[cfg(not(feature = "backlinks"))]
+    async fn test_generate_car_ephemeral_rejected() -> miette::Result<()> {
+        let tmp = tempfile::tempdir().into_diagnostic()?;
+        let mut config = crate::config::Config::default();
+        config.database_path = tmp.path().to_path_buf();
+        config.ephemeral = true;
+
+        let state = Arc::new(AppState::new(&config)?);
+        let repos = ReposControl(state);
+        let did = Did::new("did:plc:testephemeral").into_diagnostic()?;
+        let handle = repos.get(&did);
+        let res = handle.generate_car().await;
+        let Err(err) = res else {
+            panic!("generate_car in ephemeral mode should fail");
+        };
+        assert!(err.to_string().contains("ephemeral mode"));
+        Ok(())
+    }
+    #[tokio::test]
+    async fn test_generate_car_root_mismatch_fails() -> miette::Result<()> {
+        let tmp = tempfile::tempdir().into_diagnostic()?;
+        let mut config = crate::config::Config::default();
+        config.database_path = tmp.path().to_path_buf();
+        config.ephemeral = false;
+
+        let state = Arc::new(AppState::new(&config)?);
+        let did = Did::new("did:plc:testmismatch").into_diagnostic()?;
+
+        let dummy_cid = jacquard_repo::mst::util::compute_cid(b"dummy_root").into_diagnostic()?;
+        let repo_state = crate::types::RepoState {
+            root: Some(crate::types::v2::Commit {
+                version: 3,
+                rev: crate::db::types::DbTid::from(&jacquard_common::types::string::Tid::now_0()),
+                data: dummy_cid,
+                prev: None,
+                sig: bytes::Bytes::new(),
+            }),
+            ..crate::types::RepoState::synced()
+        };
+
+        let did_key = keys::repo_key(&did);
+        state
+            .db
+            .repos
+            .insert(&did_key, crate::db::ser_repo_state(&repo_state)?)
+            .into_diagnostic()?;
+
+        let repos = ReposControl(state);
+        let handle = repos.get(&did);
+
+        let res = handle.generate_car().await;
+        let Err(err) = res else {
+            panic!("generate_car with mismatched root should fail");
+        };
+        assert!(err.to_string().contains("mst root mismatch"));
+        Ok(())
+    }
 }