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| Define not coming up. Have you looked to see if they germinated and died before they broke the ground or just didn't germinate at all?
It could be getting compacted and turned anaerobic in those areas. The upper areas may not be absorbing/retaining as much water and it is running to the lower parts.
i would look at something like Agtiv (there are probably others and maybe better) which is an in-furrow inoculant ) this will provide mycorrhizal fungi, which attaches to the plants roots, and extends the root system of the plant, and absorbs and controls water in the field. For non-legumes typically azospirillium is added which is a nitrogen fixing bacteria, but it doesn't attach to the plant like the nodules in legumes. If you can identify what is causing the seed issue, like it is damping off. There are some other biological controls you can add to combat it, and provide stimulants for growth that are usually naturally there but may not be in large enough numbers because of the anaerobic conditions. As those get rebuilt in the soil, and careful care of the soil microbiology the problem will most likely start to disappear.
https://www.ptagtiv.com/en/products/agtiv-soybean-combo-liquid/
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Soybeans/ wet soils/ treflan / and seed treatments.
