There is always a chance that there was a porous seam in the clay in the excavated side of the pond. Ideally several compacted layers would be plated atop these areas (the entire basin) to prevent these leaks.
When the pond was filling, did you notice any wet spots in the basin that was NOT your incoming spring? Those wet spots may be those seams where water will go in and out depending on surrounding ground water pressure. If you have any indication where these were, you can always drain down a bit to expose those again and address them with Bennonite.
If the bennonite doesn't do the trick, Soilfloc is your next best bet.
