More trouble with STUFF
You could move the subquery into the main query and add where cht.issueid = i.issueid. Optionally you could add distinct and an order by depending on how the data are related.

SELECT
    i.IssueID AS IssueID,
    i.PAndCAuditDate AS AuditDate,
    i.PAndCValidationCompletedOn AS ValidationCompletedOnDate,
    i.CustomerIssueNumber AS OldId,
    i.PAndCValidatedBy AS ValidatedBy,
    i.PAndCValidatedComments AS ValidatedComments,
    i.Title AS Title,
    i.OpenDate AS IssueOpenDate,
    i.PAndCAuditors AS Auditors,
    i.PAndCAuditees AS Auditees,
    i.Description AS Description,
    i.PAndCRootCause AS RootCause,
    i.PAndCContainmentAndCorrectiveActions AS ContainmentAndCorrectiveActions,
    i.PAndCPreventiveActions AS PreventiveActions,
    DATEDIFF(d, i.TargetDate, GetDate()) AS DaysOverdue,
    i.TargetDate AS IssueTargetDate,
    i.ClosedDate AS IssueClosedDate,
    CASE WHEN i.ClosedDate IS NULL 
      AND DATEADD(d, DATEDIFF(d, 0, i.TargetDate), 0) 
        &lt; DATEADD(d, DATEDIFF(d, 0, GetDate()), 0) 
        THEN 1 ELSE 0 END AS IsOverdue,
    --s1.CompanyHasType
    --s1.Name
    , STUFF((
    SELECT distinct ', ' + ct.Name + ' - ' + ct.ShippingAddressCity 
        + ', ' + ct.ShippingAddressRegion + ' ' + ct.CountryID 
    FROM Company ct
     INNER JOIN PAndCIssueLocation cht ON cht.CompanyID = ct.CompanyID 
     --INNER JOIN Issue c ON c.IssueID = cht.IssueID
     where cht.IssueId = i.IssueId
     --order by ct.name
         FOR XML PATH(''), TYPE).value('.[1]',
       'nvarchar(max)'), 1, 2, '') AS CompanyHasType
FROM
    Issue i
/*LEFT JOIN
(
SELECT c.IssueID, STUFF((
    SELECT ', ' + ct.Name + ' - ' + ct.ShippingAddressCity + ', ' 
        + ct.ShippingAddressRegion + ' ' + ct.CountryID FROM Company ct
     INNER JOIN PAndCIssueLocation cht
     ON cht.CompanyID = ct.CompanyID INNER JOIN Issue c
     ON c.IssueID = cht.IssueID
         FOR XML PATH(''), TYPE).value('.[1]',
       'nvarchar(max)'), 1, 2, '') AS CompanyHasType
FROM dbo.Issue AS c
GROUP BY c.IssueID  
) s1 ON
s1.IssueID = i.IssueID
*/