The apparent bug in Twitter's service, first discovered by Favstar.fm, appears to be have affected how mentions are displayed, with some notifications being replaced by older retweets or not showing up at all.
Mentions seen in the third party app Tweetbot. | Source: Favstar.fm
Initial reports claimed the glitch was limited to Twitter's official iPhone app, however it seems the issue can be replicated in third party software as well.
Initial reports saw the glitch only in Twitter's official app.
From Favstar's blog post:
It turns out @Twitter for iPhone will sometimes not show a mention on their Connect -> Mentions tab. This seems to happen when an older mention has been retweeted by another user, which takes the place of the mention that should be there.
While the mentions are not being displayed correctly on iOS versions pulling from Twitter servers, the micro blogging company's web client has not been affected, possibly pointing to a bug in the service's API.