Instantiatied prefab runs script twice?

Hello everyone I'm having a slight problem with a instantiated prefab running a script(that is in the .prefab file) running the script attached twice. According to the Log the gameobject and the prefab instance both run the script instead of just the prefab. Now I have fixed this issue(preventing gameobject from running condition) but it still bothers me that I don't understand why this happens in the first place.

 public class CreateRegiment : MonoBehaviour

 {

     Regiment regiment;

     PlayerAIVote prefabvote;

     bool HasVoted = false;

     // Use this for initialization

     void Start ()

     {

         prefabvote = GetComponent<PlayerAIVote>();//vote instances runs in regiment GO can then vote when VotingEnabled = true

         regiment = GetComponent<Regiment>();

         regiment.Init(Country.CountryObjects[0].CompanysPerRegiment);

         regiment.DisplayAllCaptains();

         

         

     }

     

     // Update is called once per frame

     void Update ()

     {

         if(PlayerAIVote.IsReset)

         {

             HasVoted = false;

         }

         if(MissionAssignment.WindowsInstancesToBeCreated != 0 && HasVoted == false)

         {

             //votes will be logged at different times in future updates

             prefabvote.Vote(regiment);

             print ("Regiment Has Voted");

             HasVoted = true;

         }

     

     }

 }

 

 The .Vote Method simply increments a array element.

         if(regiment.Personality.CompareTo(PersonalityArray[2])==0)
         {
             print ("Peronality Detected");//Delete
             if(MissionAssignment.WindowsInstancesToBeCreated == 1)
             {
                 //if(gameObject.name != "flag")
                 //{
                     Debug.Log (string.Format ("GameObjects Running: {0}",gameObject.name));
                     print ("Vote Casted");
                     //Battle Scripts Will Combine With the Concept of Defence Rating and Offensive Rating
                     PlayerYesVotes[0]++;//Automaticly Votes Yes until battle system is created.
                 //}
             }
         }