Last night iTunes told me that I had 10 applications that were updated. However, the badge that appears on the application item under the library section in iTunes showed only 1. I went ahead and downloaded all 10 anyway. They all downloaded but no update was made to the iPod. I even pressed sync, but still nothing. I took a look in the Mobile Applications folder and now I had multiple copies of the supposedly updated apps. The updated files were labeled with a 1 at the end, for instance:
Evernote.ipa
Evernote 1.ipa
Trism.ipa
Trism 1.ipa
This is the same as what iTunes will do with music if you already have the song there and choose to keep the old version (except it'll ask you if you want to keep the old).
A quick comparison of file sizes showed that only one was different: Evernote. I ended up deleting the original apps from the Mobile Applications folder and renamed the new ones. Then I deleted the apps from the iPod, and then readded them. The problem with this is that all the of the application's data is lost when you do this! This is a major problem. I didn't lose anything important this time, but it's all going to depend on which applications get updated.
I'm curious to find out what other people have experienced, because I think the update system is broken as it is now.