When you open a parenthesis in Quarry's SQL editor and go to the next line, it gets intended by two spaces. However, when you close the parenthesis it doesn't get de-intended back to the left. (It does it for the line after the close parenthesis, but not the close parenthesis itself, resulting in unaligned pairs of parentheses).
Also if you remove the indentation inside the parentheses (or change it to something other than 2 spaces), Quarry doesn't recognize that and still does it its own way. This really doesn't help with Tidy'ing the SQL statements.
I recommend either disabling this and allowing users to indent at will, or to use a fully functional mechanism (potentially, by using an existing Tidy algorithm).