Noted

#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>

int main()
{
    //All commented out declarations are to be omitted
    //all FLAG variables to be initialized to 1 or 0 depending on later code
    int number;
    int count;
    int add = 0;
    int index;
    //int count2;
    //int index2;
    //int count3;
    //int index3;
    //int isTrue;
    //You cannot sqrt a number without first knowing what it is!
    //do the calculations INSIDE the for loop
    int squareRoot = (int)sqrt(number);
    //int isRight = 0;
    int repeatingFlag;
    int checkZeroFlag;
    int squareRootFlag;
    char stringNumber[10];
    char characterNumber;
    int repeatingArray[10]
    char numberPlaces[10];

    for (count = 111111111; count <= 999999999; count ++)
    {
        //converting to a string
        for (index = 9; index >= 0; index --)
        {
            numberPlaces[index] = number % 10;
            number = number / 10;
            stringNumber[index] = numberPlaces[index] + 48;
        }

        //setup the array to check for repeating
        //reuse index, get rid of count2
        for (count2 = 0; count2 < 10; count2 ++)
        {
            //replace: count2 with index
            repeatingArray[count2] = 0;
        }

        //checking each individual character and counting which one it is
        //reuse index, get rid of index2
        //you're mixing index2 and index here, reusing index will help lower confusion
        for (index2 = 0; index < strlen(stringNumber); index2 ++)
        {
            //replace: index2 with index
            characterNumber = stringNumber[index2];

            switch (characterNumber)
            {
                case '0':
                    repeatingArray[0]++;
                    break;
                case '1':
                    repeatingArray[1]++;
                    break;
                case '2':
                    repeatingArray[2]++;
                    break;
                case '3':
                    repeatingArray[3]++;
                    break;
                case '4':
                    repeatingArray[4]++;
                    break;
                case '5':
                    repeatingArray[5]++;
                    break;
                case '6':
                    repeatingArray[6]++;
                    break;
                case '7':
                    repeatingArray[7]++;
                    break;
                case '8':
                    repeatingArray[8]++;
                    break;
                case '9':
                    repeatingArray[9]++;
                    break;
                default:
                    break;
            }
        }

        //checking each array after counting
        //replace count3 with index
        for (count3 = 0; count3 < 10; count3++)
        {
            //replace: count3 with index
            if(repeatingArray[count3] >= 2)
            {
                repeatingFlag = 0;
            }
        }

        //checking for zeros
        //repeat index3 with index
        for (index3 = 0; index3 < 10; index3++)
        {
            //replace: index3 with index
            characterNumber = stringNumber[index3];
            if(characterNumber == '0')
                //replace: isTrue with checkZeroFlag
                isTrue = 0;
        }

        //checking if perfect square
        //PUT THE EQUATION HERE!!!
        if((squareRoot * squareRoot) == number)
            //replace: isRight with squareRootFlag
            isRight = 1;
        else
            //replace: isRight with squareRootFlag
            isRight = 0;

        if((checkZeroFlag(count) == 1) && (squareRootFlag(count) == 1) && (repeatingFlag(count) == 1))
        {
            add++;
            printf("%d. %d\n", add, count);
        }
    }
    //replace: count with 0
    return count;
}