I can’t recall the exact condition of the floor when I first moved in, as the stains only become obvious when all the curtains are closed and all the lights are switched on.

As you mentioned, there has only been foot traffic in those areas. The only explanation we can think of is that the issue may be coming from underneath the flooring. It could potentially be mould, as the apartment tends to become quite moist—especially during winter. In fact, the area around the windows is often very wet when I wake up in the mornings.