Proper reasons to downvote a question?

Question

Coming to the site, it seemed that downvotes are obvious for questions that are wildly off-topic or simply a mess (no effort in writing, badly written, unclear question, pretentious assumptions, clear misunderstanding of anything and everything ever conceived).

However, I've been seeing a lot of downvotes recently for questions that are either on-topic (specifically about the subject matter of the site) and clearly not a mess (written well, with effort, humble tome, slightly unclear question).

Are there any reasons for downvoting a question that I'm not seeing? Or should I take these as anomalies?

EDIT: I'm speaking of the Trilogy sites.

EDIT2: Yes, I do expect the downvotes of irony that this question will receive =(

Some examples of downvotes for on-topic questions:

• How can I wait for a file to be uploaded via ftp then delete it? -- A fully on-topic answer, albeit slightly badly written. Yet, I was able to understand it completely, and it has a very real answer. Surely, editing for clarity is the proper course of action here.
• What is the point of the anti-cross-domain policy? -- Well written, fully thought out, asker provides his own attempts at figuring out his problem
• How do Clojure programs/compulers/interpreters actually "work"? -- My own selfish example that may or may not have been the inspiration for this post >.>

Answer 1

Remember that the ultimate reasoning behind a downvote is "This question is unclear or not useful" or "This answer is not useful". So regardless of whether it is on-topic or nicely presented, if the content is not useful then it's quite appropriate, and quite encouraged, to point this out by downvoting it. Reasons that something may not be useful include that it promotes an incorrect pattern of thought, it has some glaring vulnerability that could be dangerous if implemented, or there are one or more errors in the content of the post.

Once you get past that, the majority of votes are anomalies like vengeance or spite. But remember there is always perspective. Never attribute to malice what can be explained by different systems or lack of experience. I cast a downvote on Stack Overflow once because the answer did not seem to address the needs of the question author. The answerer edited the answer to more clearly identify this misconception, and if I had more experience in the field I would've known it myself (and probably would've upvoted in the first place). So I undid my downvote.