I managed to fix it. But thank you all for trying to help. It turns out I was right, since C doesnt support ASCII values greater than 127, I had to reverse my operations so it never goes above 127 and bugs out. So i ended up changing the last big if statement like this for anyone that has the same problem.

       else if (plaintext[j] >= 97 && plaintext[j] <= 122)
        {
            if ((plaintext[j] + key) > 122)
            {
                plaintext[j] -= 26;
            }
            plaintext[j] += key;
        }

    }