I have been making many workflow changes lately and recently ran into a bug when I associate a new workflow to an existing project:
Issue:
After assocaiting the new workflow and remapping current issues, I would go to close a sprint I would get the "Sprint cannot be completed as there are incomplete subtasks on the following issues"
When I looked at these sub-tasks they were definitely "Done" and resolved properly. I did not want to delete these, since the sub-tasks show a history and have information of what was completed.
Work-Around:
I "moved" all of the sub-tasks having the issue to the current location they were in (project/parent). Then ensured that they were set to Done again, I was then able to close the sprint.
During the workflow change, it seems something is getting corrupt with the sub-tasks.
Yes I exclude them subtasks from my boards intentionally to reduce clutter. This only occurs when I map a new workflow to the parent issue, my workflows for the sub-tasks work fine otherwise. I probably could have adjusted the JQL filter and moved them, but still there seems to be an underlying issue here.