Use Bulk-Edit to remove the issue from any sprint. It then goes into the backlog and you can drag it to the correct one.
I'm not sure how you would have an open issue that is still in a closed sprint. Closing a sprint will move all issues that are not Done to your backlog. Example:
0 issues were Done.
2 incomplete issues will be returned to the top of the backlog.
1 partially complete issue will be returned to the top of the backlog.
Is it possible that your problem issue is not showing up right now because something has changed that means it no longer satisfies the filter for the board?
Here's an example.
Filter = "Project = W AND labels = X".
For me, when the label is missing, opening the issue and then clicking on "view on board" will give an error/response:
There are no boards which contain this issue.
This differs slightly from your reported behaviour.
But maybe it's enough to point you in the right direction?
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