One of Apple's selling points with its iOS and Mac App Stores is that it can provide a safe, trusted location for users to update their apps knowing any changes have been vetted by Apple — though in the last few days it appears some issues have been disrupting the system. Instapaper developer Marco Arment writes that when the 4.2.3 update to his popular reading app rolled out yesterday, users found that it was crashing immediately upon launch, even though the archive Arment submitted to Apple worked without issue. Several hours later, the problem was mysteriously resolved without explanation from Cupertino, but not before Arment had been contacted by users of other iOS and even Mac apps that had been experiencing similar issues over the past few days. According to Arment, the only way to resolve the issue once an app has been corrupted is to delete it entirely, and then reinstall it with a fresh, working version — assuming you have one available, that is. We've been able to confirm that several of the programs he lists — including PDX Bus and Angry Birds Space HD Free — are demonstrating the behavior, while others, such as the Mac app SmartReporter, appear to now be updating correctly.
GoodReader for iPad has also suffered at the hands of the mystery glitch, with its developers noting that the app has had the issue with two consecutive updates, including version 3.16.0 which was released just today. While we were able to update to 3.16.0 successfully, according to GoodReader's creators the problem stems from an encryption issue on the App Store side, resulting in customers receiving binaries that iOS refuses to launch. In response, GoodReader's developers have provided a lengthy tutorial on how their customers can roll back to previous working versions of the app without losing any of their GoodReader data.
We've reached out to Apple for comment, and will update you with any further details. In the meantime, you may want to refrain from updating any mission-critical apps until it's clear the situation is completely resolved.