Issues are closed automatically after "autoclose_referenced_issues" on a project is disabled

Summary

On GitLab Security, we disabled the "Auto-close referenced issues on default branch"

However, after merging some MR's into master, the issues were automatically closed:

• https://gitlab.com/gitlab-org/security/gitlab/-/issues/192#note_5e0f40873f8de5a9a01c27335a6ea2ddd0a49bb1
• https://gitlab.com/gitlab-org/security/gitlab/-/issues/223#note_22bba53d40d680bec0f29d27311eced21d9acc42

Steps to reproduce

1. Create an issue.
2. Create a merge request targeting the default branch with Closes <ID of the issue> in the merge request description
3. Disable "Auto-close referenced issues on default branch"
4. Merge the merge request

Example Project

https://gitlab.com/gitlab-org/security/gitlab

What is the current bug behavior?

Issues are closed automatically

What is the expected correct behavior?

Issues should not be closed automatically

Output of checks

This bug happens on GitLab.com

Possible fixes

(If you can, link to the line of code that might be responsible for the problem)