The textperthousand command is available both with the T1 encoding (used by classicthesis) and the TS1 encoding.. However, the Palatino font loaded via the mathpazo package by classicthesis hasn't the required glyph: in the T1 encoding textperthousand is built by adding a small zero next to % and the small zero is missing (a black square is used to show this).
Read On