Yes, words are contextual and don't always mean the same things every time they're used.
I had zero difficulty understanding the post you're replying to— and neither did you. It doesn't even annoy me any more, probably because, as a chemist, I got it out of my system years ago.
The time one of my second cousins responded to my telling her my major by making a face and saying "I don't like chemicals" does kind of stand out...
From context I’d say they mean fertilizer, pesticides, and herbicides.
Edit: you will probably find that many words have multiple meanings, and it is not hard to find words that have one specific technical meaning and a different one in colloquial usage. Organic is another common one.
What does that mean? Everything is made of chemicals.