Double closing system notes when closing issue with Merge Request

When we close a issue using our markdown on merge requests sometimes we get two system notes
one shows that issue has been closed by the merge commit and other by the merge request itself.

I noticed that this behavior is transient. Is this expected or should we pick only one?

Further duscussion: https://gitlab.com/gitlab-org/gitlab-ce/issues/19262#note_28373166