It happens sometimes - especially on Stack Overflow - that a question will receive three close votes for community-specific reasons (i.e., as off-topic), and each voter will choose a different reason. This typically indicates a very low quality and unsalvageable question that has multiple things wrong with it, but sometimes someone just chooses a bad reason, or there is some nuance to the closure reasons.
When this occurs, from what I can tell, the closure dialog will simply report:
This question does not appear to be about [site topic] within the scope defined in the help center.
In other words, this behaviour no longer appears to be reproducible, which may have something to do with changing from 5 votes required to close a question to 3. This feature continues to work on sites which retained the threshold of 5 votes: if two voters picked one community-specific close reason and at least two others picked another, then both will show in the notice. However, this is not possible on sites where the threshold to close is 3 votes, such as Stack Overflow.
This result is not helpful and is usually misleading. Questions like this aren't "off-topic" in the general sense of the word; they just don't meet the site's standards. The dialog should instead explicitly indicate that multiple issues were identified that make the question close-worthy.
This is not a duplicate of Distinguish close votes by reason because that question refers to distinguishing votes for different top-level reasons (duplicate, needs more focus, needs details/clarity, etc.). That feature doesn't exist, and that's a request for that feature to be added. This question, on the other hand, asks for the already-existing functionality of showing multiple close votes to be improved to work better on sites only requiring three votes to close a question.
ORDER BY
with no fallback for tie-breakers is often a cause). It could very well be intentional, as you suggest, and if so, I really don't know why it would be. If you can point me to an example where there are 3/5 unique reasons (depending on site), I can quickly examine the query.