I work for Microsoft in the TFS group. Your symptoms could be a result of data corruption in TFVC. I suggest you file a support ticket with Microsoft. Here are some links for that. The first is for on-premises TFS and the second is for our cloud service.
https://www.visualstudio.com/support/support-overview-vs
https://www.visualstudio.com/en-us/support/cloud-services-assisted-support-vs
If you prefer you can contact me directly (wlennon at Microsoft.com) and I can give you a SQL query to run to determine if it's data corruption or not.
Also, you can look in the EventViewer on your SQL Server machine for more details about this error. Look for a message like this:
Cannot insert duplicate key row in object 'dbo.tbl_LabelEntry' with unique index 'PK_tbl_LabelEntry'