aeroseo

Запускайте слайдер, когда открывается всплывашка

$('.open-popup-link').magnificPopup({
     
  type:'inline',
  midClick: true, // Allow opening popup on middle mouse click. Always set it to true if you don't provide alternative source in href.
});
$('.open-popup-link').click(function(){
var swiper = new Swiper('.swiper-container', {
            spaceBetween: 0,
            centeredSlides: true,
            autoplay: {
              delay: 400,
              disableOnInteraction: false,
            },
            pagination: {
              el: '.swiper-pagination',
              clickable: true,
            },
            navigation: {
              nextEl: '.swiper-button-next',
              prevEl: '.swiper-button-prev',
            },
          });
});

Вот так попробуйте.