Accessing other scripts from prefab instances isn't allowed?

I’m just beginning with learning Unity and I feel a bit silly about needing to ask this.

I have a very basic set-up where I have a prefab of a target and instances of that target are instantiated faster and faster. The prefab has a script where the object is destroyed if it is clicked (using on mouse down). I want your score to increase every time you click a target but I have no clue to do this. I currently have a separate game object called “ScoreTracker” with a script that has the score variable I want to update, but Unity doesn’t seem to let you put references to other scripts into prefabs (if anyone knows why, please explain because I’d love to learn about it) so I can’t update the score from the prefab instance itself. I’ve tried researching this but have concluded that I must be doing something completely wrong and I’m not sure what to do. So, how is something like this usually handled?

You’re fine, you have to learn to even know how it’s done so don’t feel silly. I can kind of try to explain it but I don’t want to confuse you so I’ll share some video tutorials from YouTube.
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How to detect an object with mouse click in Unity: Click on object with Raycast screen - Unity [ENG] - YouTube
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After you got reference to the object you just clicked, you can get any information you need about it. For example, if the object has a Rigidbody on it then you can get reference to it as follows:
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Rigidbody prefabBody = hit.collider.gameObject.GetComponent();
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Then anything you do to the variable prefabBody will happen to the GameObject you referenced
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Another good tutorial I found: Selecting Objects in the 3D World with the Mouse Using Raycast (Unity Tutorial) - YouTube