In the general case, this is working as intended. Specifically, it's intentional that we accept linebreaks in the middle of a "Fixes X, Y" statement, because linebreaks aren't always added explicitly by users.

In this specific case, we could conceivably exclude statements containing multiple consecutive internal linebreaks, but that would still allow the user to accidentally close tasks with a single newline.

You can reconfigure maniphest.statuses to adjust the "prefixes" keywords. For example, you could change them into command strings like "phabricator-fixes" instead of "fixes", which would require users to write Phabricator-fixes T123 instead of Fixes T123. Note that these prefixes are not fully configurable (see T5132). This is not a change we're interested in pursuing in the upstream, because the feedback we receive about this feature is overwhelmingly that it is highly desirable in its current form.

From a user point of view, this won't happen if you write commit messages in natural language (for example, See T93645 for discussion. won't trigger this). Alternatively, Ref T93645 (vs bare T93645) will trigger Phabricator to create a stronger "reference" relationship instead of a weak/implicit "mention" relationship.

Finally, you can disable "Autoclose" for the repository to stop all automatic relationships.