Checking TODOs in comments is not persisting them

When we click on a TODO item that is part of the issue/merge request description it works, but when doing the same thing with TODO items inside a comment, it displays itself as checked, the API response is successful, but reloading the page shows up that its not being persisted.

It looks like this is due to ActiveRecord::QueryCanceled, as we recently reduced from 5s to 2s on GitLab.com.