A sample way of using sub query here would be as
SELECT QuarterWk.Week,CountOfBatchID,SumOfDocAcc,TotalErr,ErrPerBatch,QuarterWk.Quarter
FROM
(SELECT QuarterWk.Week, Count(WkCounterMFG.BatchID) AS CountOfBatchID, Sum(WkCounterMFG.DocAcc) AS SumOfDocAcc, NZ(Sum([#TotalObs]),0) AS TotalErr, IIf(Count([BatchID])=0,0,[TotalErr]/Count([BatchID])) AS ErrPerBatch, QuarterWk.Quarter
FROM QuarterWk LEFT JOIN WkCounterMFG ON QuarterWk.Week = WkCounterMFG.RepWk
GROUP BY QuarterWk.Week, QuarterWk.Quarter
HAVING (((QuarterWk.Quarter) Like [Forms]![RFTWkRepFormMFG]![Quarter]))
);
and if you want anly the count, then you can use this
SELECT CountOfBatchID
FROM
(SELECT QuarterWk.Week, Count(WkCounterMFG.BatchID) AS CountOfBatchID, Sum(WkCounterMFG.DocAcc) AS SumOfDocAcc, NZ(Sum([#TotalObs]),0) AS TotalErr, IIf(Count([BatchID])=0,0,[TotalErr]/Count([BatchID])) AS ErrPerBatch, QuarterWk.Quarter
FROM QuarterWk LEFT JOIN WkCounterMFG ON QuarterWk.Week = WkCounterMFG.RepWk
GROUP BY QuarterWk.Week, QuarterWk.Quarter
HAVING (((QuarterWk.Quarter) Like [Forms]![RFTWkRepFormMFG]![Quarter]))
);