"No database selected" or "Table 'DB.table' doesn't exist" failures in pt-upgrade run where queries from multiple DBs were collected with tcpdump
Does it still fail to work if you omit --sample?
(from manual)



  Also note that pt-query-digest may fail to report the database for
  queries when parsing tcpdump output. The database is discovered only
  in the initial connect events for a new client or when  is
  executed. If the tcpdump output contains neither of these, then
  pt-query-digest cannot discover the database.



Consider using the general log instead of tcpdump?