From your brief description, I assume you have configured some form of Repository trigger in your plan and Bamboo fails to trigger a new build based on your changes in the repository - thereby resulting in code coverage not getting completed. Correct me if I understood it wrong.
If the repository is in Bitbucket server, we should be able to see something like this in atlassian-bamboo.log:
If you don't see this, you would have to contact Atlassian Support to confirm if the issue is with connectivity or with Bamboo performance.
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