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Description
In some cases git will not know that a branch has been merged because your local version of the branch differs from the copy of the branch that was merged.
For example, let's say User A checked out Branch A, then User B checked out Branch A and rebased it to squash some of the commits into a larger commit, then User B merges Branch A into the default branch (let's say master) and deletes Branch A from your GitHub/GitLab repo. git on User A's machine doesn't think Branch A was merged into master because the commit SHA of the latest commit on User A's copy of Branch A doesn't match any of the commits that are now in master.
Unfortunately I'm not sure of a good way to fix this issue, short of adding a flag that would let you delete any branches without upstream counterparts (this would have the side effect of deleting local branches you haven't pushed yet, which isn't great).