Issue symptoms
Why is the organization tag overwriting a user tag, when the tags belong to a custom ticket field, under the tag values?
Resolution steps
Zendesk adds organization and user tags to tickets when the ticket is created. However, if you are using a custom field with the same tag values and the custom field value isn't selected, a race condition may overwrite one of the tags.
The organization tag usually overwrites the user tag. However, in some cases, the user tag might overwrite the organization tag due that same race condition.
To avoid facing this race condition, use different tags for organizations and users on any custom field.
For more information, see these articles: User and organization tags in business rules and Using custom fields.