what i was doing wrong was not grouping the result set by ta.minbenchmark and ta.maxbenchmark. hence it would only get the results for the first min-max pair it finds technically making the having clause ineffective. So the correct query would be as follows (for anyone making the same mistake):
SELECT p_date,TS.substationid,ts.substationcode,ts.manufacturingproductid,ts.assemblylineid,ts.teamid,ts.subofficecode,
TA.AllowID,ta.allowname,ta.minbenchmark,ta.maxbenchmark,COUNT(vfp.UnitsPass) Achieved,
CASE TA.RewardType
WHEN 'Monthly' THEN
TA.RewardValue/DAY(LAST_DAY(P_Date))
WHEN 'Yearly' THEN
TA.RewardValue/((STR_TO_DATE(CONCAT(EXTRACT(YEAR FROM P_Date),1,1),'%Y%m%d')) /(STR_TO_DATE(CONCAT(EXTRACT(YEAR FROM P_Date),12,31), '%Y%m%d')))
WHEN 'Daily' THEN
(TA.RewardValue*12)/365
END-- , 0)
AS Allowance
FROM tempsubstation ts
LEFT JOIN TempAllowances ta ON ts.manufacturingproductid=ta.manufacturingproductid AND ts.subofficecode=ta.subofficecode
LEFT JOIN wms_vfproduction vfp ON DATE(vfp.CreationDate)=p_date AND vfp.StationCode='1600150'
WHERE ta.AllowID=41 AND vfp.UnitsPass=1
GROUP BY p_date,substationcode,ta.minbenchmark,ta.maxbenchmark
HAVING COUNT(vfp.UnitsPass) BETWEEN ta.minbenchmark AND ta.maxbenchmark
;