This sounds more like a quirk/limitation of Sony’s interval shooting in S mode than a lens fault. Community experience suggests many Sony bodies don’t handle aperture changes normally during interval shooting in Shutter Priority; some effectively lock or mis-handle aperture from the first frame rather than opening up as light falls.

So while it’s not the behavior you’d expect from ordinary S mode, it’s likely an interval-shooting implementation issue rather than a broken camera or Sigma lens.

For day-to-night timelapses, the more reliable workaround is to shoot in Manual exposure with Auto ISO, so shutter speed and aperture stay where you want them while ISO adapts as light changes. That tends to be the recommended Sony approach for transitional timelapses.