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If someone has a similar problem, I was able to solve the issue by restoring the original window options this way: 
 cy.on('window:before:load', (win) => {
    win.setTimeout = window.setTimeout;
    win.setInterval = window.setInterval;
    win.requestAnimationFrame = window.requestAnimationFrame;
    win.clearTimeout = window.clearTimeout;
    win.clearInterval = window.clearInterval;
  })
  cy.visit();