MYSQL joining 3 tables with left join
I suggest you first read this question and answer Help with this query. 

Then try to rewrite your queries using Option 3 (or all of the options). The following is a first attempt at option 1:

SELECT 
    p.id_pupil
  , p.name
  , p.surname
  , ROUND(AVG(q.calificacion),2) AS average
  , COUNT(DISTINCT q.id_qualification) AS count
  , COUNT(DISTINCT CASE WHEN i.type_incident = 'miss'        THEN i.id_incidents END)
       AS misses
  , COUNT(DISTINCT CASE WHEN i.type_incident = 'delay'       THEN i.id_incidents END)
       AS delays
  , COUNT(DISTINCT CASE WHEN i.type_incident = 'attitude'    THEN i.id_incidents END)
       AS attitude
  , COUNT(DISTINCT CASE WHEN i.type_incident = 'miss_justif' THEN i.id_incidents END)
       AS misses_justificadas
FROM 
    pupils                   AS p 
    LEFT JOIN incidents      AS i  ON  i.id_pupil = p.id_pupil
                                   AND i.id_trimester = 1
    LEFT JOIN qualifications AS q  ON  q.id_pupil = p.id_pupil
                                   AND q.id_trimester = 1
                                   AND q.type_qualification = 'class' 
WHERE 
    p.level = 1
    AND p.class = 'A' 
    AND p.id_trimester = 1 
GROUP BY 
    p.id_pupil 
  , p.name
  , p.surname ;