I am using two boards in a single JIRA project according to this, and used different filters for each board. Is it possible to filter 'Burndown chart' by same filters as well?
For example, Board 1 is filtered for Assignee A, and Board 2 is filtered for Assignee B. And when I go to Burndown chart report, I want to see the report for Assignee A only if I choose Board 1.
In this case, I would ask you to first open any issue that is showing up on both boards. Check the values in the *Sprint Field*. Does this with Assignee A attached to a sprint from Board B? If so, this could be the reason why you are seeing this issue in both reports.
If this is not the case, then you would need to do a lock reindex in Jira as this may just be an issue with corrupted indexes.