diff --git a/src/cfnlint/runner.py b/src/cfnlint/runner.py
index 706fe84309..442ff91b24 100644
--- a/src/cfnlint/runner.py
+++ b/src/cfnlint/runner.py
@@ -293,12 +293,9 @@ def _validate_filenames(self, filenames: Sequence[str | None]) -> Iterator[Match
                     "E0000".startswith(x) for x in self.config.ignore_checks
                 ):
                     matches = [match for match in matches if match.rule.id != "E0000"]
-                    if matches:
-                        yield from iter(matches)
-                    return
-                else:
-                    yield from iter(matches)
-                    return
+
+                yield from iter(matches)
+                continue
             yield from self.validate_template(filename, template)  # type: ignore[arg-type] # noqa: E501
 
     def validate_template(
diff --git a/test/unit/module/runner/test_run.py b/test/unit/module/runner/test_run.py
new file mode 100644
index 0000000000..06d7734e1b
--- /dev/null
+++ b/test/unit/module/runner/test_run.py
@@ -0,0 +1,55 @@
+"""
+Copyright Amazon.com, Inc. or its affiliates. All Rights Reserved.
+SPDX-License-Identifier: MIT-0
+"""
+
+import pytest
+
+from cfnlint.config import ConfigMixIn
+from cfnlint.runner import Runner
+
+
+@pytest.mark.parametrize(
+    "name,config,expected_count",
+    [
+        (
+            "Test decode errors with multiple files",
+            ConfigMixIn(
+                cli_args=[
+                    "--template",
+                    "test/fixtures/templates/bad/duplicate.yaml",
+                    "test/fixtures/templates/bad/duplicate.json",
+                ]
+            ),
+            6,
+        ),
+        (
+            "Test decode errors with E0000 being ignored",
+            ConfigMixIn(
+                cli_args=[
+                    "--template",
+                    "test/fixtures/templates/bad/core/parse_invalid_map.yaml",
+                    "--ignore-bad-template",
+                ]
+            ),
+            0,
+        ),
+        (
+            "Test decode return E0000 errors",
+            ConfigMixIn(
+                cli_args=[
+                    "--template",
+                    "test/fixtures/templates/bad/core/parse_invalid_map.yaml",
+                ]
+            ),
+            1,
+        ),
+    ],
+)
+def test_run(name, config, expected_count):
+
+    runner = Runner(config)
+
+    errs = list(runner.run())
+
+    assert len(errs) == expected_count, f"{name}: {errs}"