Concerning your last paragraph, well, that would be my guess too, this should be taken to MSE as it won't be solved on a per-site basis. It likely has been discussed over there already.
It could be (however remote the chances really are) that this is by design, as in judging the close-worthiness of the question strictly without its answers; e.g. a question that is clearly off-topic should be closed no matter how good and on spot the answers are. Note that closing a question with answers does not necessarily deletes the question (certain restrictions apply):
How does deleting work? What can cause a post to be deleted, and what does that actually mean? What are the criteria for deletion?
- The system will automatically delete closed, unlocked questions with zero or negative score having no positively scored or accepted answers or pending reopen votes, that were closed for any reason other than duplicate nine or more days ago and haven't been edited in the past nine days. (RemoveAbandonedClosed)
So if there are any good answers to a question you would consider close-worthy consider giving the answre an upvote and vote close on the question. This way we get the best of the situation: that particular question stays on the site (while being closed) and the rules of site are "enforced", thus setting repeatedly a precedence what the community here deems appropriate content.