It's important to manually check your spam filter. Spam filters are never perfect, and they always require some degree of user intervention to train them to properly identify spam (both preventing false negatives and false positives).
If you are noticing a systemic problem though (I am not, my spam filter seems to be working fine and I only rarely have messages get misclassified) then perhaps you have a problem with Akismet and you could look into filing a bug report with that system.
One thing that I have noticed, however, is a huge increase in the volume of spam lately. I used to only rarely get spam and I got 6 spam messages in the past week or so. So it could be that if there is an increase in spam, this is causing an increase in false positives.
Also, don't assume that your comments are getting marked as spam just because they don't post. I always moderate comments on all my blogs, not just because of spam but because of other comments that I don't want to post for various reasons, like I think they contain misinformation that I don't think is worth publishing, or I find them disrespectful. Sometimes it can take me several days to moderate and post even the comments I do want to publish.