All options provided describe valid ways in which two substances can be different:
A. Two substances can be composed of the same chemical elements, but the substances can have crystal structures with atoms that are arranged differently. (This refers to different allotropes or polymorphs of a substance.)
B. Two substances can be composed of different chemical elements. (This is a direct and clear distinction between two substances.)
C. Two substances can be composed of molecules that contain the same chemical elements but have different numbers of atoms of each element. (This refers to different compounds or molecular formulas, such as glucose (C6H12O6) and fructose (C6H12O6), which contain the same elements but are arranged differently.)
Therefore, all the options (A, B, and C) are ways in which two substances can be different.