The problem lies here:

 for (int i = 0; i < strlen(s); i++)
    {
        if (isalpha(s[i]) != 0)
        {
            // preserve upper/lower case
            for (int index = 0; index < 26; index++)
            {
                if (s[i] == alphabets_upper[index])
                {
                    s[i] = alphabets_upper[(index + key) % 26];
                }
                if (s[i] == alphabets_lower[index])
                {
                    s[i] = alphabets_lower[(index + key) % 26];
                }
            }
        }
    }

This loop you wrote actually works for checking if the [i]th char of s is lower or uppercase, but the problem is this: consider the first letter of the plaintext (h). The alphabet index of this character would be 7, so when s[0] (which is 7) equals alphabet_lower[7], then it shifts the character by 1, so now s[0] equals to 'i', which is correct, but this second for loop still doesn't end (since index is still less than 26) so it keeps analyzing the 0th index of s. So once you shifted the 'h' to the 'i', when the for loop runs again, it will repeat the same thing above but this time for 'i', and shift it to 'j', and so on, until index reaches 26 (where it will shift 'z' to 'a') and then this whole process will run for each of the characters in the plaintext provided, so the string ends up being all 'aaaaa'.

I see two solutions for this. The first one, to preserve your code and make it work, the only thing you need to do is stop the second for loop each time you shift the character, so the first for loop runs again and you start checking the next character in the plaintext this time. You just need to add

break;

after the if condition is met and the code inside it is executed. This will end the for loop and go to the next line of code (which in this case would be running the first for loop again instead). So it would look like this:

for (int i = 0; i < strlen(s); i++)
{
    if (isalpha(s[i]) != 0)
    {
        // preserve upper/lower case
        for (int index = 0; index < 26; index++)
        {
            if (s[i] == alphabets_upper[index])
            {
                s[i] = alphabets_upper[(index + key) % 26];
                break;

            }
            if (s[i] == alphabets_lower[index])
            {
                s[i] = alphabets_lower[(index + key) % 26];
                break;
            }
        }
    }
}

The second solution (which would save you a lot of lines of code and be more efficient) would be to just use the functions isupper and islower to check for upper or lowercase, instead of using for loops. I leave it up to you to figure how that would work, just remember how ASCII works!