Move the wait to after the animation starts. You probably also want to have it inside the clips test, and update bullets left after the wait is over.

function Reload () {    
    if (clips > 0) {
        clips--;
        animation.Play ("Reload");
        yield WaitForSeconds(reloadTime);
        bulletsLeft = bulletsPerClip;
    }
}

If it would help you understand the flow of code, let's break down the Reload function into smaller parts:

function Reload ()
{
    if (clips > 0) 
    {
        BeginReload();
        yield WaitForSeconds(reloadTime);
        EndReload();
    }
}

function BeginReload () 
{
    clips--;
    animation.Play("Reload");
}

function EndReload () 
{
    bulletsLeft = bulletsPerClip;
}