I am trying to understand a few more details about the scenario that you are describing.
In general, in Agile a defect should be either opened as part of a user story acceptance test or for a specific feature, for example, when a test fails during a regression cycle.
In the first case the acceptance test for the defect is actually the user story's acceptance test that was failed in Agile Manager, in this case I recommend to mark the user story as blocked, to mark the relevant acceptance test as failed and to link the defect to the user story.
In the second case the test that failed is the test that needs to be executed when the defect is fixed.
Another possible scenario is that the QA team logs a defect that actually covers a functional area that was not part of the feature scope. In this case this defect should be replaced with a user story and the user story should be managed in Agile Manager as any other user story.
Please share your thoughts and use case around that.