Could iron-based formula be upsetting my baby's stomach?

No. I think this is unlikely but commonly believed, there is less iron in formula than in breast milk for example. It is more likely to be some other issue... Such as lactose intolerance or perhaps milk allergy.
No. Although this was a common belief in the past studies have shown that the iron available in formula does not trigger upsets. Much of the bad RAP likely relates to iron drops that are necessary for those infants with anemia. The high iron content occasionaly bothers those infants. Without iron, baby can't build the new blood cells needed for growing tissue.
No. Iron-based formula should not upset a baby's stomach. Babies need iron, so the commercial formulas have iron in them. A baby with an upset stomach more likely has another reason for the tummy problem. Thus. The parents should talk with the doctor about the baby's symptoms.