Usando várias consultas aninhadas no Oracle DBMS

SELECT Email, Phonenumber
FROM EMPLOYEE
WHERE COUNT(
ID = (SELECT ID_Num
FROM SCHEDULE
WHERE Start_Time <= 12:07 AND End_Time >= 12:07)
AND Shopn = (SELECT Shopname
FROM SHOP
WHERE Shoptype = ‘market’) ) > 2

1. Parece que você está tentando selecionar o id usando o operador "=", que falhará no caso de várias entradas retornadas pela consulta interna.
2. Você não pode adicionar operadores agregados na cláusula where.

select Email, Phonenumber
FROM EMPLOYEE
WHERE ID in (SELECT ID_Num
FROM SCHEDULE
WHERE Start_Time <= '12:07' AND End_Time >= '12:07')
AND Shopn in (SELECT Shopname
FROM SHOP
WHERE Shoptype = 'market')
and (  
select count(distinct id)
FROM EMPLOYEE
WHERE ID in (SELECT ID_Num
FROM SCHEDULE
WHERE Start_Time <= '12:07' AND End_Time >= '12:07')
AND Shopn in (SELECT Shopname
FROM SHOP
WHERE Shoptype = 'market')) > 2;