Använd FIND_IN_SET() funktion:
Prova detta:
SELECT A.allocationId,
B.className,
GROUP_CONCAT(C.subjectShortName) AS subjectName
FROM subjectAllocation A
INNER JOIN class_Master B ON A.classId = B.classId
INNER JOIN subject_Master C ON FIND_IN_SET(C.subjectId, A.subjectId)
GROUP BY A.allocationId;