If you are using new ARM deployment model for creating Traffic Manager then you may run into this error which is not very descriptive but essentially this is because Azure Internal Endpoints are not supported yet by the API/Cmdlet. You could fix this by changing endpoint type to -Type “ExternalEndpoints” parameter in the endpoint cmd, more details about this limitation is here
Set-AzureTrafficManagerProfile : BadRequest: The resource target ID property of endpoint 'NorthEurope' is invalid or missing. The property must be specified only for the following endpoint types: AzureEndpoints ,NestedEndpoints. You must have read access to the resource to which it refers.