What does it mean when a weed plant has the seed growing on top instead of from the root?

This is totally normal. What you have noticed is epigeal (above ground) and hypogeal (below ground) seeds. When you plant a Pea seed, the seed splits, a tiny root grows down deeper into the soil and then it starts pushing a stem out above ground. The original seed stays in the ground and you don't see it. When you plant a bean seed, the root grows first, then it pushes up a stem above ground, just like the pea. Only Beans are epigeal, meaning the original seed stays on top of the first two leaves that you see. Eventually, the halves of the seed end up somewhere on the lower section of the plant stem and then wither up and usually fall off. You also see this in chives and onions from seed. If the two plants you are growing are identical species, then you probably just didn't notice the seed shell on the one that you think doesn't have it. Whether the seed shell stays in the ground or grows with the stem for a short time is totally dependent on species. So if you planted two different plant species, then it's entirely possible that one is epigeal and one is hypogeal. Way to be observant! I never even noticed a difference until it was pointed out to me in a botany lab (and I'm a horticulture major!)

It's normal, don't worry. It's just managed to punch out (and up) the husk of the shell that it sprouted from. When it grew, it busted the shell of the seed and carried some of the seed casing that was simply hanging on to the new sprout. Happy gardening!