MySQL slow log logs every query instead of just slow queries
Maybe your mysqld got it's long_query_time value from another source. What happens if you run:

select @@long_query_time;


Note that I would consider setting the long_query_time to 0 to be good practice, particularly on Innodb databases. Consider the case where query A takes 1 second and runs a thousand times a day vs query B taking 20 seconds and run once a day; you'll get more benefit from tuning query A.