Several possible reasons at wikiHow:
The leaves on my pomegranate are turning yellow. Why?
During the growing seasons of spring to early fall, this may be an indication of insufficient or too much watering. Like most plants, pomegranate trees need the right balance of moisture to grow well. Limit watering as the season changes from summer to fall, allowing the soil to dry out before watering again; after all, pomegranate is a desert plant and it's used to aridity. On the other hand, when the plant is first establishing itself in the ground after transplanting, it needs regular waterings to help the roots take hold. This might be another reason for yellowing of the leaves, so be sure to keep a transplanted tree well watered at least twice a week. Other reasons for yellowing leaves can include sap sucking insects, too much fertilizer or insufficient nitrogen and the cooling temperatures. In the latter case of falling temperatures, this is the normal cycle for the pomegranate, which is a deciduous tree and it will lose it leaves in late fall. If the plant appears otherwise healthy and it's late fall, assume that all is normal.
A bigger pot would seem called for and give you the opportunity to see if rootbound. I suspect not enough water.