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This happens quite frequently on reddit as well. I'd imagine it's due to the fact that the set of people who vote on a story are different than the set who vote on comments. For example, people could find a title appealing and upvote without actually reading the article or any of the comments. At the same time, the people who take the time to read the article (and corresponding comments) vote up the comments criticising the article. Since it takes relatively more time to read and understand an article, the knee-jerk reaction voters cause the story to be highly rated even though the top comment is critical.

It seems lile that could be fixed by tracking which articles a user clicks and disregard an upvote if they didnt read the story or they read it 5 seconds ago.

What if they already read the story from a different source?

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