All plants contain chemicals that are healthful and chemicals that can harm us. Fortunately for us, our ancestors learned which plants are edible and healthful, and taught us to avoid those that are poisonous to humans. However, if you eat very large amounts of one food, you can poison yourself, even though reasonable amounts are harmless or beneficial.
For example, soybeans contain genistein, a weak estrogen that may help to prevent breast cancer. They contain omega-3 fatty acids that help prevent heart attacks, and are loaded with fiber that helps to prevent diabetes. But they also contain small amounts of trypsin inhibitors that increase risk for pancreatic damage and cancer in animals. Hemagglutinins in soybeans could cause clots to form and travel to the lungs. Goitrogens in soybeans block thyroid function to increase your need for that hormone. Estrogen-like genistein in soybeans could stimulate immature lobules in breast tissue of infants to increase risk for breast cancer many years later. Phytates in soybeans and many other plants can block the absorption of minerals.
However, you would need to eat very large amounts of soy products to get any of these negative effects. Enjoy a moderate amount of soy foods, but do not let health claims lead you to eat huge amounts of soy to the exclusion of other foods. A healthful diet is a varied diet.