I have a feeling that the word "ingredient" implies that it was intended to be there by human, while catechin is not an additive, but was naturally in the tea leaves. Giving another example, is polyphenol a healthy ingredient of wine, a composition, or a compound of wine?
Catechin is a compound itself in chemistry, more specifically a polyphenolic compound. It is not a compound of another thing. I wouldn't use ingredient, composition or component either. Constituent makes the most sense if you are talking about a chemical compound:
A constituent of a mixture, substance, or system is one of the things from which it is formed.
Caffeine is the active constituent of drinks such as tea and coffee.
Although, it is better to explain in a way that catechin is something, a compound, found in green tea. A usual way to say is:
Catechin is a naturally occuring compound found in green tea.
I think you're looking for the word component.
A compound is something made up of other things, as is a composition, so those words would far more readily describe green tea than catechin.
I agree that ingredient tends to imply human agency, though that implication is perhaps not absolute.
Component fits the bill nicely, however.
Your subtle question is interesting. As a reader, I don't think I would be misled by the phrase, "a naturally occurring ingredient in tea leaves" or the same phrase using a synonym for ingredient like element or component although I do share your reluctance to use ingredient or its synonyms all by themselves. You are obviously a very careful writer. I think you can trust your instincts.
Merriam-Webster Unabridged defines ingredient as:
ingredient, noun : something that enters into a compound or is a component part of any combination or mixture : constituent
and gives as an example usage:
[A] formula which will have just about the same ingredients as mother's milk
which in no way implies that mother's milk contains any additives.
As for polyphenols in wine:
Wine's polyphenols come from grapes, mainly from the skins, and because the red-winemaking process involves more extended contact with the grape skins, those wines tend to contain a lot more polyphenols than white wines do.
So polyphenols are a component, or ingredient, of wine that comes from the fruit from which wine is made.
In a similar manner, catechins are indeed an ingredient, or component, of green tea.
noun in·gre·di·ent in-ˈgrē-dē-ənt Synonyms of ingredient : something that enters into a compound or is a component part of any combination or mixture : constituent
INGREDIENT applies to any of the substances which when combined form a particular mixture. (emphasis mine)
in early use also engredient, early 15c., "something forming part of a mixture," from Latin ingredientem (nominative ingrediens) "that which enters into" (a compound, recipe, etc.), present participle of ingredi "go in, enter," from in- "in" (from PIE root *en "in") + gradi "to step, go" (from PIE root *ghredh- "to walk, go"). Also from early 15c. as an adjective, "forming part of a mixture." (emphasis mine)
There might be some documentation to support the idea that the long-running and historical use of this term requires things to be man-made, but my quick scan doesn't reveal it. That being said, given that a number of people here believe it to be a necessary condition of the definition, it may be that a new sense of the word is developing or is undocumented, and that you share the new sense with others. For the record, I don't have the same association with man-made being part of the "essence" of the word.
Of ingredient, composition, and compound, only the first and last work with 'ingredient' emphasizing it's role as a part, and 'compound' emphasizing it's non-elemental nature. (Chemical compounds are systems of atomic elements.)