MySQL Seleccionar consulta para obtener la base de registros en los valores de la lista

Use FIND_IN_SET() función:

Prueba esto:

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;