It could well be cleat placement. I have bunions, and I suffered from foot pain for years, trying to figure out the cause. Riding for more than an hour or two was very painful. The first podiatrist said I needed surgery, but it's a painful ordeal, and I would have needed to be totally off my feet for several weeks. The second podiatrist I saw said, "I know these feet," as if he was talking about a year, make, and model of a car. He told me to ride with stiff shoes and to move my cleats back. Now my pain is 90-95% abated. My cleats are very far back, putting my arches over the pedal spindles. It was weird at first. I had to lower my saddle to accommodate this.

But everyone is different. Seek the help of an expert or several experts. A fit expert at a bike shop might be able to help.