Why are some natural/organic brands rated "not clean" on your app?

That's something you should ask them. We don't look at brand names, we only take the ingredients and match them with our sources to give you opinions based on all studies from governments, scientific communities, and non-profit groups.
The word "Natural" lacks clear legal definitions. The word "Organic" has some precise meanings depending on the regulations of the countries.
So in some cases, just because a brand is called organic, it doesn't mean it's truly natural. That's why reading labels by scanning is so important.