Toddler help

My son just turned 2 and has low iron and low vitamin D.  He eats a very healthy diet and he plays outside a lot.  I am at a loss as to why he is having this problem.  He eats mostly vegetables and fruits, fortified cereal oatmeal, lots or beans and peanut butter.  He also has a large soft spot on the top of his head.  The pediatrician said he might have a problem with mineralization.  But does not think the soft spot is related.  He is also seeing a neurosurgeon.  Does anyone on here know anything about absorption of nutrients or have a toddler with a soft spot (about the size of a half dollar).? We won't have a follow up for 6 weeks and this is just breaking my heart.  If anyone could shed some light on this I would appreciate it!