Yael I pulled all our stuff out last week and noticed the exact same thing. Caro is right, it's more than likely milk that turns yellow over time when the clothes are stored away.

Just wash them as normal in Amolin (or lux flakes, or whatever you use for bubs clothes) and hang them directly in the sun for the day - the sun will remove the stains 99% of the time. It's worked on all of my stuff so far.