Don't worry. Brush daily and not once in 2 days. Brush well. The stains could be related to what your son is taking daily over the course of the day...for example, formula milk, syrups, and other food items. Nothing needs to be done at this stage. Good brushing might get rid of these stains.
Next Steps
Keep a check on the teeth and see a pedodontist (pediatric dentist) when you think it is getting worse.
Health Tips
I appreciate the fact that you noticed the stains and are worried enough to post your concern here. Keep up the same attention for you son's teeth as well as your teeth and those of your other family members.