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There are a few places that I would start searching to debug the issue.
1.) You can check the logs from the different containers of MWAA, to see if the item is being expressed through the logs. If there is a problem stopping the metrics from getting to CloudWatch, it will most definitely be mentioned in the logs. (Networking, permissions, etc.)
2.) You can review CloudTrail, specifically for any errors occurring from the Username: AmazonMWAA-airflow, this is the username taken by the execution role. If there are API errors in CloudTrail, this could be what is stopping your metrics from being uploaded in time.
3.) Check to ensure that your installed packages aren't causing conflicts with other dependencies or the Airflow program itself. Ensure you use a constraints line as suggested in our documentation best practices 1. This ensures that no packages get installed that can conflict with Airflow packages, or other Python packages that the environment uses (this can break functionalities, and doesn't always surface right away).
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