Сделайте, чтобы каждый из вас выбирал общее табличное выражение, затем полностью внешнее объедините их вместе:
WITH cte1 AS (SELECT mam.fecha AS fecha,
u.COD_USUARIO AS usuario,
u.NOMBREAPELLIDOS AS nombre,
ROW_NUMBER() OVER (PARTITION BY u.cod_usuario
ORDER BY mam.fecha ASC) AS rn_asc,
ROW_NUMBER() OVER (PARTITION BY u.cod_usuario
ORDER BY mam.fecha DESC) AS rn_desc,
mam.accion AS accion,
u.ID_CENTRO_GESTION AS centrogestion
FROM r_mod_asignar_material mam
INNER JOIN r_usuarios u
ON mam.cod_usuario = u.cod_usuario
where mam.ACCION = 'A' and
trunc(mam.fecha) = to_date('13/09/2018','dd/mm/yyyy') AND
mam.cod_usuario = '9717703' AND
u.id_centro_gestion = '3'
order by u.cod_usuario),
cte2 AS (SELECT mam.fecha AS fecha,
u.COD_USUARIO AS usuario,
u.NOMBREAPELLIDOS AS nombre,
ROW_NUMBER() OVER (PARTITION BY u.cod_usuario
ORDER BY mam.fecha ASC) AS rn_asc,
ROW_NUMBER() OVER (PARTITION BY u.cod_usuario
ORDER BY mam.fecha DESC) AS rn_desc,
mam.accion AS accion
u.ID_CENTRO_GESTION AS centrogestion
FROM r_mod_asignar_material mam
INNER JOIN r_usuarios u
ON mam.cod_usuario = u.cod_usuario
where mam.ACCION = 'D' and
trunc(mam.fecha) = to_date('13/09/2018','dd/mm/yyyy') AND
mam.cod_usuario = '9717703' AND
u.id_centro_gestion = '3'
order by u.cod_usuario),
cte3 AS (SELECT COUNT (*) numeroincidencias,
ri.cod_usuario usuario
FROM r_incidencias ri
WHERE TRUNC (ri.fecha_inc) = TO_DATE ('13/09/2018', 'dd/mm/yyyy') AND
ri.cod_usuario = '9717703'
GROUP BY ri.cod_usuario)
SELECT *
FROM cte1
FULL OUTER JOIN cte2
ON cte2.cod_usuario = cte1.cod_usuario
FULL OUTER JOIN cte3
ON cte3.cod_usuario = COALESCE(cte1.cod_usuario, cte2.cod_usuario)