multiple count and use subsctract function in one query
Without seeing the exact error message returned, I can't be 100% certain, but there are two glaring errors:

Is the column name Department or Dept?  This does not seem clear.
You cannot reference tot1 unless it is first derived in a CTE or sub-select (derived table).
The subquery sum(select count(status_mcu) where status_mcu='done') does not have a FROM clause.  Furthermore, I'm not sure what purpose where aggregating a high-level aggregate is necessary/desired.
As a general critique, you're hitting the same table over and over again which is not optimal from a performance standpoint.

Start with this and see if it returns the desired results (if it doesn't, you'll need to clarify your question to provide the proper logic):
SELECT
  mcu.Dept
 ,COUNT(mcu.Id) AS Tot1
 ,SUM
    (
      CASE
        WHEN mcu.status_mcu='done' THEN 1
        ELSE 0
      END
    ) AS tot2
 ,COUNT(mcu.Id) - 
    SUM
      (
        CASE
          WHEN mcu.status_mcu='done' THEN 1
          ELSE 0
        END
      ) AS tot3
FROM
  mcu mcu
GROUP BY
  mcu.Dept