mysqltuner.pl shows [!!] 2 different collations for database
No, it is not a problem. The documentation sums things up.


  Every table has a table character set and a table collation. The
  CREATE TABLE and ALTER TABLE statements have optional clauses for
  specifying the table character set and collation


The default database character set/collation values are used for a table if the relevant clauses are not specified at table creation time.