Identifying root cause of slow query outliers from pt-query-digest?
Queries can become slow in such cases:


server is shorted out with disk i/o
server is shorted out with memory and swapped
server have too small key_buffer_size and buffer should be refreshed prior to perform the query
server have too small (join|sort)_buffer_size and on-disk temporary tables are created


Any of the mentioned above can cause sporadical slowdown. List is not exhaustive, sure.