Learning to identify different egg masses in vernal pools is a great way of knowing which species are breeding there. Our top three vernal pool amphibians in Central New York are wood frogs, yellow-spotted salamanders, and Jefferson’s salamanders. Other species might use them, too, if it is a pool that doesn’t dry up completely. These could include leopard frogs and pickerel frogs. From your description, it sounds like you either found two different species’ eggs, or the eggs were just in different stages of development. Wood frogs, especially, lay their eggs in communal masses over the course of a few weeks, so it might be that the darker egg spots were more developed. Pickerel frogs have a lighter colored embryo, and their eggs are not perfectly round.
Here’s a website with great information on identifying amphibian eggs in vernal pools. I hope it helps to solve your mystery!