Error when overriding only some audio shortcode HTML output

This should work, regardless how many tags you have in the post, and regardless which have whatever attributes. My guesses are either the logic in your handler is slightly off, or a 3rd party (i.e. plugin) is hijacking the default shortcode handler behaviour.

To test, remove your code and try the following – it should clearly demonstrate if (or if not) the default shortcode & filter is working as expected:

function wpse_209708_debug_audio_shortcode( $html, $attr ) {
    if ( ! empty( $attr['player'] ) && $attr['player'] === 'default' )
        $html="{audio player:default}";
    else
        $html="{audio player:other}";

    return "<p>$html</p>";
}

add_filter( 'wp_audio_shortcode_override', 'wpse_209708_debug_audio_shortcode', 10, 2 );

Report back and I will update this with a “real” answer.