This is usually due to damping off, a symptom caused by several diseases. If damping off doesn't kill seedlings it is likely to delay seedling emergence. McWilliams says temperatures below 60 degrees, water-saturated soils, and sealed soil surfaces are stresses on soybeans that can contribute to damping off.
Deep planting can also play a role.
She recommends a planting depth for soybeans of one to one and one-half inches, with a maximum depth of two inches. McWilliams cites a University of Illinois study of relative emergence of soybeans planted at different depths. The one-inch depth had the greatest emergence and was set at 100 percent for comparison purposes. The relative emergence for the three-fourths inch planting depth was 85.5 percent of maximum. Move soybeans carefully in cold weather, especially when loading or unloading in bags or running beans through augers.