Pirate seal full - go to harbour and get commissions. What does that mean?

Some ports will let you pick up commissions which are small side missions to trade certain goods or sink armed freighters or others that let you earn some points for the guilds influence.

To accept a commission you need a use a Pirate seal, these will generate over time (up to a set maximum) and when they are full the game reminds you to go and use them.