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Using node.destroy_subscription(subscription) is the "right way" to do things. It seems like you're encountering a bug, could you include a bit more error context (maybe just more of the console output even if it doesn't seem relevant)?

It's also useful to have a minimal example that could replicate the issue.

If you want to open an issue against https://github.com/ros2/rclpy/issues, I think this would be appropriate given that you're doing the right thing, just getting an unexpected error.

Also, since this question is a bit old (sorry), maybe you solved it already?