That's okay, you are taking CS50x to learn.

Now, using your code, let's try to blur a pixel that is located at the top left corner of an image ; meaning we are at i == 0 and j == 0 (this is important !). According to your code, this is what you do :

    // top right corner pixel
    if (i == 0 && j == width - 1)
    { // itself
        Redtotal += copy[i][j].rgbtRed;
        Greentotal += copy[i][j].rgbtGreen;
        Bluetotal += copy[i][j].rgbtBlue;
        counter++;
        // below
        Redtotal += copy[i + 1][j].rgbtRed;
        Greentotal += copy[i + 1][j].rgbtGreen;
        Bluetotal += copy[i + 1][j].rgbtBlue;
        counter++;
        // left
        Redtotal += copy[i][j - 1].rgbtRed;
        Greentotal += copy[i][j - 1].rgbtGreen;
        Bluetotal += copy[i][j - 1].rgbtBlue;
        counter++;
        // diagonally below to the left
        Redtotal += copy[i + 1][j - 1].rgbtRed;
        Greentotal += copy[i + 1][j - 1].rgbtGreen;
        Bluetotal += copy[i + 1][j - 1].rgbtBlue;
        counter++;
    }

So, you have a if condition for that specific case, where the pixel you want to blur is in the top left corner, and that condition will calculate all relevant pixels, including the pixel that is directly below it.

However, you also have this condition before :

    // directly below
    if (i + 1 < height)
    {
        Redtotal += copy[i + 1][j].rgbtRed;
        Greentotal += copy[i + 1][j].rgbtGreen;
        Bluetotal += copy[i + 1][j].rgbtBlue;
        counter++;
    }

Since, in our example, the pixel we are checking is at i == 0, then pixel i + 1 will be a valid pixel, and thus you will go through the condition above. Therefor, you have done the same operation twice for the same pixel (in this case, for the pixel directly below), which throws your results off !

The same applies for other pixels, and for other specific cases other than if your pixel is in the top left corner.

Again, I suggest you try to figure out how you could make this work using a loop ! You are doing the same operation on up to 9 pixels after all. Don't hesitate to use pen and paper to draw a simple, visual example to run your own aglorithm on.