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I don't know whether this is necessarily the cause of your issue, but I discovered one reason why it doesn't always work. On mobile Safari, iOS ends up inserting smart quote characters rather than straight quotes when you type them. Google ends up ignoring the smart quote characters. To work around this, I have to hold down the " button to explicitly make the keyboard insert the straight quote character.

Are you saying that it was returning pages that didn't contain the phrase "the onion", or just weren't articles from The Onion? What was the exact search term?

Does that happen for words that aren't likely stopwords?