How do I make instantiated prefabs independent?

I have 2 scripts. 1 of them is when is the user left clicks, a target prefab is created where the mouse was clicked and a missile prefab is created at a certain location. The second script is attached to the missile prefab where it will move towards the target and then explode.

Left clicking quickly will create missile prefabs but will travel at the same location when they haven’t exploded - acting as if they are the same. How do I instantiate a prefab that is independent from the other missiles?

Provide the script and we can answer your question. It seems easy enough but we want to make sure we know what exactly you mean.