Edit: Here's my code.

Edit2: Latest code (working)

int main (int argc, string argv[])
{
    // Checking for proper command line input
    if (argc != 2)
    {
        printf("Usage: ./substituion key\n");
        return 1;
    }

    // Checking for 26 character input key
    if (strlen(argv[1]) != 26)
    {
        printf("Key must contain 26 characters.\n");
        return 1;
    }

    // Checking for alphabetic input
    for (int i = 0; i < 26; i++)
    {
        if (argv[1][i] >= 'a' && argv[1][i] <= 'z')
        {
            argv[1][i] = argv[1][i];
        }
        else if (argv[1][i] >= 'A' && argv[1][i] <= 'Z')
        {
            argv[1][i] = argv[1][i];
        }
        else
        {
            printf("Key must only contain alphabetic characters.\n");
            return 1;
        }
    }

    // Checking for repeated characters
    for (int i = 0; i < 26; i++)
    {
        for (int j = 25; j > i; j--)
        {
            if (argv[1][i] == argv[1][j])
            {
                printf("Key must not contain repeated characters.\n");
                return 1;
            }
        }
    }

    // Removing key's sensitiity
    for (int i = 0; i < 26; i++)
    {
        if (argv[1][i] >= 'A' && argv[1][i] <= 'Z')
        {
            argv[1][i] = argv[1][i];
        }
        else
        {
            argv[1][i] -= 32;
        }
    }


    // Getting plaintext input
    string message = get_string("plaintext: ");

    // Substitution of plaintext to key
    for (int i = 0, n = strlen(message); i < n; i++)
    {
        for (int j = 0; j < 26; j++)
        {
            if (message[i] == j + 'A')
            {
                message[i] = argv[1][j];
                j = 26;
            }
            else if (message [i] == j +'a')
            {
                message[i] = argv[1][j] + 32;
                j = 26;
            }
        }
    }

    // Ciphertext
    printf("ciphertext: %s\n", message);
    return 0;
}

[OUTDATED/ANSWERED] Edit: Here's my code.

Edit: Here's my code.

#include <ctype.h>
#include <cs50.h>
#include <stdlib.h>
#include <stdio.h>
#include <string.h>

int main (int command, string line[])
{
    // Checking for proper command line input
    if (command == 2)
    {
        // Checking for 26 character input key
        if (strlen(line[1]) == 26)
        {
            // Checking for alphabetic input
            for (int i = 0; i < 26; i++)
            {
                if (line[1][i] >= 'a' && line[1][i] <= 'z')
                {
                    line[1][i] = line[1][i];
                }
                else if (line[1][i] >= 'A' && line[1][i] <= 'Z')
                {
                    line[1][i] = line[1][i];
                }
                else
                {
                    printf("Key must only contain alphabetic characters.\n");
                    return 1;
                }
            }

            // Checking for repeated characters
            for (int i = 0; i < 26; i++)
            {
                for (int j = 25; j > i; j--)
                {
                    if (line[1][i] == line[1][j])
                    {
                        printf("Key must not contain repeated characters.\n");
                        return 1;
                    }
                }
            }

            // Getting plaintext input
            string message = get_string("plaintext: ");

            // Substitution of plaintext to key
            for (int i = 0, n = strlen(message); i < n; i++)
            {
                for (int j = 0; j < 26; j++)
                {
                    if (message[i] == j + 'A')
                    {
                        message[i] = line[1][j];
                        j = 26;
                    }
                    else if (message [i] == j +'a')
                    {
                        message[i] = line[1][j] + 32;
                        j = 26;
                    }
                }
            }

            printf("ciphertext: %s\n", message);
            return 0;
        }
        else
        {
            printf("Key must contain 26 characters.\n");
            return 1;
        }
    }
    else
    {
        printf("Usage: ./substituion key\n");
        return 1;
    }
}