Hello! By uneven teeth you mean they have different shades of colour in the same teeth or they are unevenly positioned? If the prior then it could be due to
calcium deficiency or other factors such as fluoride deficiency or excess. If the latter, then it is not due to calcium deficiency but due to the pattern of eruption. Permanent teeth erupt at different ages, so right now your son has both milk teeth & permanent teeth in his mouth. By the age of 12-13years all the permanent teeth will have erupted except the wisdom teeth, so if till then also the teeth do not align themselves correctly, your son will have to undergo orthodontic (braces) treatment.
Next Steps
For now, you can visit a dentist who can advise you if your son needs any appliance till all his permanent teeth have erupted to guide their eruption.