Add a warning when someone adds <ref> tags in MassMessage to remind users to include <references/> in their message (or one of the templates with the same functionality like {{talkrefs}}).
When using Extension:MassMessaging, if you add a reference using <ref> tags, the reference always appears at the bottom of the talk page, even if others add new sections after your message. People often don't know how to fix that.
This would warn users that, if they want to use references, they should also use <references/> or {{talkrefs}} to ensure the reference stays with the message.
Prohibiting MassMessages to contain refs is also fine, if that is the preferred solution.
This could use the existing system in /modules/ext.MassMessage.badhtml.js which outputs warnings when it detects unbalanced tags.