Mysql slow query log Not filtering correctly

If you setup mysql's slow query log you might notice it not filtering on the value setup up for the global variable long_query_time. For example maybe you have this setup for a value of 2 seconds, but are seeing durations of 0 or 1 seconds being recorded. The most likely reason for this is the variable "log_queries_not_using_indexes" is turned on by default and this uses the same log file or log table as the slow_query_log.