Change in bone structures is the best thing i could think of.
Be careful of the terms you use.
Chemicals with the same chemical composition but different structures are called isomers.
The specific example you gave of diamond and graphite suggests that you're looking for different forms of elements that have different physical structures. Those are called allotropes.
A waste product is a product that is made but isn’t necessarily needed eg. A lightbulb will make light energy but it also makes a waste product heat.
