That's what just happened to me with Opera. A matter of days after Opera 10.52 was released, version 10.53 appeared in response to the discovery of an "extremely severe" vulnerability that meant "Multiple asynchronous document modifications can be used to execute arbitrary code". The problem only affects the Windows and Mac OS X versions.
I'm all in favour of updates and patches being released promptly, so I'm not complaining about the timing.
But I am slightly worried that this afternoon, when I launched 10.52 for the first time, the Check for Updates command told me the browser was up to date. I knew that was wrong, so I checked again and this time was told that 10.53 was available.
It's also somewhat frustrating that the update involves downloading the entire 16MB installer, rather than just a patch.