Unexpected slow queries
"0.002" sounds like the Query cache came into play.

When the QC is turned on exactly the same SELECT is run a second time before any changes happen to the table(s) involved, the resultset is looked up in a Hash (called the Query Cache).  This will take on the order of 1ms regardless of how long the query normally takes.

Or...

Since you are using MyISAM, virtually any operation that touches the same table(s) will 'lock' the table and cause a normally fast query to stall for as long as the other query (or queries) take.  Switching to InnoDB is likely to help.

If you would like to discuss it further, please provide the query, SHOW CREATE TABLE and EXPLAIN SELECT ..., SHOW VARIABLES LIKE 'query%';,   SHOW GLOBAL STATUS LIKE 'Qc%';  The infomation in those may lead to eliminating one or the other of the above explanations.