Steps to reproduce
Log in as an admin. On the edit page of a canonical tag, use the "Synonym of" field to syn that canonical tag to another tag, existing or not. This bug is intermittent, so it may take several tries to trigger it.
Periodically, all the connections from the old canonical tag are not transferred to the new tag. This includes metatags, subtags, synonyms, and other child tags. It's most obvious with fandom and character tags, which tend to have a lot of child tags. With fandom tags, this results in all the child tags and synonyms appearing in the mass bins again, as they have lost their fandom connection.
What should happen
All tag connections from the canonical should be transferred to the tag it is synned to, whether that tag is newly created or existed before.
Because this bug does not always happen, testing should be conducted on many tags.