diff --git a/autograder/services/pre_flight_service.py b/autograder/services/pre_flight_service.py
index f5a0301..b8bbb5d 100644
--- a/autograder/services/pre_flight_service.py
+++ b/autograder/services/pre_flight_service.py
@@ -94,7 +94,7 @@ def check_required_files(self, submission_files) -> bool:
         for file in self.required_files:
             if file not in submission_files:
                 error_msg = t("preflight.error.required_file_missing", locale=self.locale, file=file)
-                self.logger.error(error_msg)
+                self.logger.warning(error_msg)
                 self.fatal_errors.append(PreflightError(
                     type=PreflightCheckType.FILE_CHECK,
                     message=error_msg,
@@ -142,7 +142,7 @@ def check_setup_commands(self, sandbox: SandboxContainer) -> bool:
                     command = command_spec
 
                 error_msg = self._format_command_error(command_name, command, response)
-                self.logger.error(error_msg)
+                self.logger.warning(error_msg)
                 self.fatal_errors.append(PreflightError(
                     type=PreflightCheckType.SETUP_COMMAND,
                     message=error_msg,