1. You have entered some blacklist keywords in Settings -> Discussion. When a comment matches any of those keywords, WordPress puts the comment in spam and bypasses Akismet.
2. If Akismet tries to check a comment but it fails (e.g., because the Akismet server takes too long to respond, or your API key fails to validate, or there is a connection failure), then it puts the comment in the moderation queue, and tries to check it again later (6 hours later, to be precise). If, later, the server reports that the comment is spam, then it moves the comment to spam. Obviously at this stage it is too late to show the commenter a captcha… so it stays in spam.
(2) above happens quite frequently – I have no idea why.