diff --git a/src/codemodder/codemods/libcst_transformer.py b/src/codemodder/codemods/libcst_transformer.py
index f9488ff5..671d51e1 100644
--- a/src/codemodder/codemods/libcst_transformer.py
+++ b/src/codemodder/codemods/libcst_transformer.py
@@ -263,19 +263,18 @@ def apply(
                 with open(file_path, "r", encoding="utf-8") as f:
                     source_tree = cst.parse_module(f.read())
         except Exception:
-            file_context.add_failure(file_path)
-            logger.exception("error parsing file %s", file_path)
+            file_context.add_failure(file_path, reason := "Failed to parse file")
+            logger.exception("%s %s", reason, file_path)
             return None
 
         tree = source_tree
-
         try:
             with file_context.timer.measure("transform"):
                 for transformer in self.transformers:
                     tree = transformer.transform(tree, results, file_context)
         except Exception:
-            file_context.add_failure(file_path)
-            logger.exception("error transforming file %s", file_path)
+            file_context.add_failure(file_path, reason := "Failed to transform file")
+            logger.exception("%s %s", reason, file_path)
             return None
 
         if not file_context.codemod_changes:
diff --git a/src/codemodder/file_context.py b/src/codemodder/file_context.py
index cf9d0c7d..36ed7d1e 100644
--- a/src/codemodder/file_context.py
+++ b/src/codemodder/file_context.py
@@ -31,8 +31,9 @@ def add_dependency(self, dependency: Dependency):
     def add_changeset(self, result: ChangeSet):
         self.changesets.append(result)
 
-    def add_failure(self, filename: Path):
+    def add_failure(self, filename: Path, reason: str):
         self.failures.append(filename)
+        self.add_unfixed_findings(self.get_all_findings(), reason, 0)
 
     def add_unfixed_findings(
         self, findings: list[Finding], reason: str, line_number: int | None = None
@@ -58,3 +59,10 @@ def get_findings_for_location(self, line_number: int):
             )
             and result.finding is not None
         ]
+
+    def get_all_findings(self):
+        return [
+            result.finding
+            for result in (self.results or [])
+            if result.finding is not None
+        ]
diff --git a/tests/test_libcst_transformer.py b/tests/test_libcst_transformer.py
index c848f3cb..078f933e 100644
--- a/tests/test_libcst_transformer.py
+++ b/tests/test_libcst_transformer.py
@@ -4,39 +4,98 @@
     LibcstResultTransformer,
     LibcstTransformerPipeline,
 )
+from codemodder.context import CodemodExecutionContext
+from codemodder.file_context import FileContext
+from core_codemods.defectdojo.results import DefectDojoResult
 
 
-def test_parse_error(mocker, caplog):
-    mocker.patch(
-        "codemodder.codemods.libcst_transformer.cst.parse_module",
-        side_effect=ParserSyntaxError,
+def _apply_and_assert(mocker, transformer):
+    file_context = FileContext("home", mocker.MagicMock())
+    execution_context = CodemodExecutionContext(
+        directory=mocker.MagicMock(),
+        dry_run=True,
+        verbose=False,
+        registry=mocker.MagicMock(),
+        repo_manager=mocker.MagicMock(),
+        path_include=[],
+        path_exclude=[],
+    )
+    pipeline = LibcstTransformerPipeline(transformer)
+    pipeline.apply(
+        context=execution_context,
+        file_context=file_context,
+        results=None,
     )
+    assert len(file_context.failures) == 1
+    assert file_context.unfixed_findings == []
 
-    transformer = mocker.MagicMock(spec=LibcstResultTransformer)
-    file_context = mocker.MagicMock()
 
+def _apply_and_assert_with_tool(mocker, transformer, reason):
+    file_path = mocker.MagicMock()
+    file_context = FileContext(
+        "home",
+        file_path,
+        results=[
+            DefectDojoResult.from_finding(
+                {
+                    "id": 1,
+                    "title": "python.django.security.audit.secure-cookies.django-secure-set-cookie",
+                    "file_path": file_path,
+                    "line": 2,
+                },
+            )
+        ],
+    )
+    execution_context = CodemodExecutionContext(
+        directory=mocker.MagicMock(),
+        dry_run=True,
+        verbose=False,
+        registry=mocker.MagicMock(),
+        repo_manager=mocker.MagicMock(),
+        path_include=[],
+        path_exclude=[],
+        tool_result_files_map={"sonar": ["results.json"]},
+    )
     pipeline = LibcstTransformerPipeline(transformer)
     pipeline.apply(
-        context=mocker.MagicMock(),
+        context=execution_context,
         file_context=file_context,
         results=None,
     )
+    assert len(file_context.failures) == 1
+    assert len(file_context.unfixed_findings) == 1
+    assert file_context.unfixed_findings[0].reason == reason
 
-    file_context.add_failure.assert_called_once()
-    assert "error parsing file" in caplog.text
+
+def test_parse_error(mocker, caplog):
+    mocker.patch(
+        "codemodder.codemods.libcst_transformer.cst.parse_module",
+        side_effect=ParserSyntaxError,
+    )
+    transformer = mocker.MagicMock(spec=LibcstResultTransformer)
+    _apply_and_assert(mocker, transformer)
+    assert "Failed to parse file" in caplog.text
 
 
 def test_transformer_error(mocker, caplog):
     transformer = mocker.MagicMock(spec=LibcstResultTransformer)
     transformer.transform.side_effect = ParserSyntaxError
-    file_context = mocker.MagicMock()
+    _apply_and_assert(mocker, transformer)
+    assert "Failed to transform file" in caplog.text
 
-    pipeline = LibcstTransformerPipeline(transformer)
-    pipeline.apply(
-        context=mocker.MagicMock(),
-        file_context=file_context,
-        results=None,
+
+def test_parse_error_with_tool(mocker, caplog):
+    mocker.patch(
+        "codemodder.codemods.libcst_transformer.cst.parse_module",
+        side_effect=ParserSyntaxError,
     )
+    transformer = mocker.MagicMock(spec=LibcstResultTransformer)
+    _apply_and_assert_with_tool(mocker, transformer, "Failed to parse file")
+    assert "Failed to parse file" in caplog.text
 
-    file_context.add_failure.assert_called_once()
-    assert "error transforming file" in caplog.text
+
+def test_transformer_error_with_tool(mocker, caplog):
+    transformer = mocker.MagicMock(spec=LibcstResultTransformer)
+    transformer.transform.side_effect = ParserSyntaxError
+    _apply_and_assert_with_tool(mocker, transformer, "Failed to transform file")
+    assert "Failed to transform file" in caplog.text