Bean sprouts generally come from mung beans, which are relatively harmless, but many countries in Asia use soy sprouts. Soy is the worst of the legumes, containing high amounts of anti-nutrients such as phytic acid. Soy beans are also very high in the polyunsaturated fat, omega-6, which is highly inflammatory and results in digestive issues for many people who eat them.
If you’re eating bean sprouts from mung beans and don’t experience any ill effects, there’s no reason to fear a few bean sprouts in your soup at your favorite Asian restaurant, but stay away from soy whenever possible. Mark Sisson has explained on his blog why bean sprouts are not as harmful as most other legumes.