I'm not really sure what could be wrong but my first thought is to look up symptoms of overdose of the supplements she is taking.
This is what I've found:
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Early symptoms of iron overdose
Diarrhea (may contain blood)
fever.
nausea.
stomach pain or cramping (sharp)
vomiting, severe (may contain blood)
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Vitamin D Warnings
Vitamin D could cause an allergic skin reaction. Tell your doctor if you have any allergies before taking this supplement.
This vitamin may also affect your blood sugar levels. If you have diabetes, your physician may need to monitor you while you're taking vitamin D.
Also, tell your doctor if you currently have, or have ever had, any of the following:
High or low blood pressure
Kidney problems and kidney stones
An immune disorder
Heart disease or other heart problem
Lung disorders
Thyroid problems
Liver disease
Frequent headaches
Stomach issues
Skin disorders
Musculoskeletal disorders
Vitamin D Toxicity
Although uncommon, excessive amounts of vitamin D in the body can lead to toxicity.
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So talk to your pediatrician ASAP and stop giving her the supplements for now.
Usually 15 minutes out in sunshine per day is all the exposure a human needs to be able to produce their own vitamin D so I'm not sure why a child would need a supplement for that.
Additional:
I'm glad a doctor is monitoring the supplements.
That being said - what ever the prescribed dose is still sounds too high for her.
Perhaps she needs lower/lowest doses in order to absorb what she needs without her systems going haywire.
It might take some time to get things right but if taking these supplements is the only thing that has changed in the last few weeks, then it seems to me that it's the supplements that are causing her aches and pains.
I've had doctors swear to me that the side effects I was having couldn't be caused by the medication I was taking.
But if I took the med - I had problems - if I didn't take the med - I didn't have those problems.
That solves it for me no matter what the doctor says.