du kan helt enkelt subtrahera två frågor eller slå samman
select (select query) - (select query);
SET @numberOfUsers := 0;
SELECT l.totalUsers-a.monthlyusers FROM (SELECT T.createdMonth,
T.monthlyusers, (@numberOfUsers := @numberOfUsers + T.monthlyusers) AS totalUsers
FROM
(
SELECT MONTH(FROM_UNIXTIME(u.createdDate)) AS createdMonth, COUNT(u.id) AS monthlyusers
FROM USER u
WHERE YEAR(FROM_UNIXTIME(u.createdDate)) = '2016'
GROUP BY MONTH(FROM_UNIXTIME(u.createdDate))
) T ) l,(SELECT MONTH(FROM_UNIXTIME(lastActive)), (COUNT(u.id)) AS activeUsers FROM USER u
WHERE YEAR(FROM_UNIXTIME(lastActive)) = '2016'
GROUP BY MONTH(FROM_UNIXTIME(lastActive))) a ;