Update: the problem has now been fixed.
A bug in development versions of WordPress is causing some comments to be incorrectly caught as spam. The problem is in WordPress, not Akismet, and there’s no way for Akismet to prevent it from happening.
The problem only affects WordPress blogs running current development code. It does not affect other applications that use Akismet.
Technically-minded users can read the specifics in the WordPress Trac system.
We expect to have a fix in WordPress core soon, and deployed to WordPress.com shortly after.
This is probably a good opportunity to remind readers that Akismet is not necessarily the reason a comment gets caught as spam. The majority of complaints we receive about real comments being caught as spam were in fact not caused by Akismet at all – but by other spam filtering plugins or features. (Unfortunately WordPress doesn’t show the reason a comment was moved to the Spam filter, so there’s no easy way to tell which ones were put there by Akismet and which ones by something else).
In particular, the WordPress Comment Blacklist feature (Settings / Discussion) trips up some users. It lets administrators provide a list of words, IP or email addresses that should be blocked as spam. Any comments that match words in the blacklist will automatically be moved to the Spam filter – regardless of whether or not Akismet considers it to be spam. The blacklist matches within words, meaning that if you add a short string such as “ru”, it will block any comment containing the words “truth” or “fruit”, or any other word with the letters “ru”. And, since the blacklist takes precedence over Akismet, reporting those comments to Akismet as false positives won’t stop them from being caught.
If you think the Comment Blacklist feature might be catching legitimate comments as spam, the tw-blacklight plugin might help your diagnosis.
We’ll update the Akismet blog when the WordPress bug has been fixed.
Akismet 
I great feature would be the ability to tag spam comments with the mechanism that marked it as spam.
Jonno, thanks, this is something we’re hoping to improve as well. Spam filtering aside, WordPress records very little information about comments beyond that supplied by the user – there is no record of when a comment is edited by an administrator, for example.
Why does the WordPress core have anti-spam if all WordPress installations comes with Akismet by default? It doesn’t make any sense to me.
Akismet isn’t active by default on WordPress blogs – it needs an API key. The WordPress code in question is very old and probably pre-dates Akismet. Disabling it is one possibility, but that’s up to the WordPress dev team to decide.
I haven’t noticed this kind of behavior on my self hosted blog. Rarely some comments get into spam which is okay as far as I am concerned. Thanks for all the good work!
I’ve had 2 legit posts tagged as spam by Akismet — out of several 1,000 caught successfully. That’s a fair trade-off far as I’m concerned.
I think I would have discontinued blogging early on had it not been for Akismet; the plug-in is an extremely helpful asset.
John Barremore
Houston, TX
I’ve had this problem since day one. I’m kind of new to wordpress (been using it for about a month) so I didn’t really know it was an actual bug. I’ve made it a habit to physically check Akismet since half of my comments marked as spam are legitimate comments.
Tellie, the problem has only existed for a few days and affects only a small number of comments. It should be fixed now, we’re testing to be sure.
Also, regarding the comments you’re marking as not spam, you should read this.
I have a question, if anyone can answer:
Can I mark someone as a spam and block that person from ever visiting the website? Like his computer IP would be blocked?
Rafael, there’s no way to stop one particular person from visiting your web site. That’s a bit like trying to stop one particular person from reading the newspaper. You can ask your web hosting company about ways to block their IP, but that blocks a network address, not a person.
I’ve just installed 2.2.4. Does it mean that the problem above has been completely solved?
Benny, the fix for the WordPress bug is in WordPress – and yes it has been fixed (see the update at the top of the post).
The Akismet 2.2.4 release doesn’t fix the WordPress bug, because the problem wasn’t with Akismet.
I am glad you got that fixed. That is been a problem for a while on my blog. I did not realize it was a wordpress problem.