Hi Cori, while the seed is the same and the water and nutrients seem to be the same, there is probably still some difference that is causing the second one to be stumpy. Are you sure it's getting the same amount of water? Maybe there's a pebble under the second seed. Or a tree root under it sucking up nutrients. Or a sparrow pecked at the seedling when it was little and it set it back. Or any number of other things.
I'll plant a row of 10 squash and often get a runt or two. Now I put 2-3 seeds in each place where I want a squash and cull the weakest one once there is a clear winner. Squash seeds are usually abundant so I've learned to be liberal with them.