why does medications have side effects?

They are substances not natural to us (and this goes for herbal remedies as well as pharmacological medicines) so are likely to affect our own physiology is various ways as well as the intended one.

Because everything has side effects.

Medications have side effects because they are prescribed to target certain body functions,the only way they work is to get into your bloodstream. Your blood flow throughout your whole body, delivering the medication to not only the target but everywhere, even places it is not needed..