Custom Upload Adds Ghost File

I’ve modified your code a little to check that the post type is a page, that the current user can edit that page, verify the nonce and verify the inserting attachment functions. The resulting code is working. It seems that don’t checking the post type could be the reason of the issue. Also, you don’t need to manually include ‘wp-admin/includes/image.php’:

add_filter('post_edit_form_tag', function() {
    echo ' enctype="multipart/form-data"';
});

add_action( 'save_post', 'save_custom_meta_boxes', 10, 2 );
function save_custom_meta_boxes( $post_id, $post ) {

    // If we're not in the right place, bailout
    if( ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE ) || ! isset( $post_id ) || $post->post_type !== 'page' || ! current_user_can( 'edit_page', $post_id ) ) {
        return;
    }

    if ( !isset( $_POST['page_meta_nonce'] ) || ! wp_verify_nonce( $_POST['page_meta_nonce'], 'page_meta_metabox' ) ) {
        return;
    }

    if( ! empty( $_FILES['_uploaded_file']['name'] ) ) {  
        $uploadStatus   = wp_handle_upload( $_FILES['_uploaded_file'], array( 'test_form' => false ) );
        if ( $uploadStatus && ! isset( $uploadStatus['error'] ) ) {
            $fileID         = wp_insert_attachment( array(
                    'post_mime_type'    => $uploadStatus['type'],
                    'post_title'        => preg_replace( '/\.[^.]+$/', '', basename( $uploadStatus['file'] ) ),
                    'post_content'      => '',
                    'post_status'       => 'inherit'
                ),
                $uploadStatus['file'],
                $post_id
            );

            if( $fileID ) {
                $attachmentData = wp_generate_attachment_metadata( $fileID, $uploadStatus['file'] );
                wp_update_attachment_metadata( $fileID,  $attachmentData );
                update_post_meta( $post_id, '_uploaded_file', $fileID );
            }
        }
    }
}

add_action( 'add_meta_boxes_page', 'page_meta' );
function page_meta() {
    add_meta_box("page_upload_image", 'Upload image', 'page_meta_cb');
}
/** `page_meta` Callback Function **/
function page_meta_cb( $post ) { 
    wp_nonce_field( 'page_meta_metabox', 'page_meta_nonce' );
    $uploaded_file_id = get_post_meta( $post->ID, '_uploaded_file', true );
  ?>

  <div>

    <table style="width:100%;">
        <tbody>
            <tr id="uploaded_file">
                <td style="width:8%;min-width:105px;">
                    <label for="uploaded_file_input" style="font-weight:bold;">Uploaded File</label><br />
                </td>
                <td>
                    <input type="file" style="width:100%;" name="_uploaded_file" value="" id="uploaded_file_input" />

                    <?php if( is_numeric( $uploaded_file_id ) ) : ?>

                        <div class="fileLink">
                            <a href="https://wordpress.stackexchange.com/questions/185839/post.php?post=<?php echo $uploaded_file_id; ?>&action=edit" target="_blank">Edit File - <?php echo get_the_title( $uploaded_file_id ); ?></a>
                                <br />
                                <br />
                        </div>

                    <?php endif; ?>

                </td>
            </tr>
        </tbody>
    </table>

    </div>

  <?php
} // END Metabox