'Bree' means several different things in Scots. A disturbance is one. It can also mean a soup or broth. One of the restaurants in Glasgow that the writers and producers frequent is called Barley Bree - and in this case it means whiskey.
The whiskey still was created by the art department, and it is an actual working still. However, no whiskey had been produced from it as of the airing.
Jamie's comment about the smudge being an 'unforgivable mistake by the printer' is a call back to his past career as a printer.
As time goes on, you can see that little changes are made to Young Ian's clothing. The costume department started to include small Cherokee touches like the arm band and the red porcupine quills on his jacket to show the relationship he's building with the Native Americans.
This story from Jamie's time fostering at Leoch can be found in the book Outlander. It didn't make it into the first season but fit well in this scene. The writers often save book moments that don't make it into a particular season and include them in later episodes/seasons.