We do. The most obvious example is read meat (which is now officially designated cancerogene), a bit less obvious is various "natural" herbal medications that induce renal failure [1] and cancer [2]. People consumed those substances for centuries, only to find out recently that they are harmful.
[1]: https://www.hindawi.com/journals/crim/2015/150204/
[2]: http://www.telegraph.co.uk/news/health/1343598/Chinese-herb-...