Thinking deeper on the issue, I remembered that I occasionally updated apps on my iPhone, while other times I would update the apps through iTunes. Thus, I theorized that the problem was most likely a sync conflict. We know that application syncing is two-way. So if both the iPhone and iTunes are saying that they have an updated version, it’s possible that that could be the source of the error.

So, I tested my theory out. First, I went through my iPhone and removed all the applications listed in the error message. For those that don’t know, you can remove an app on your iPhone by touch-holding any app for a couple of seconds. This makes all the application icons start to dance about and little X’s appear on the top left corner of all non-native iPhone apps. Tap the little X icon to remove the app.

Next, I went into iTunes and to the Applications list under Library. I removed the same apps here by selecting each at a time and hitting the delete key on the keyboard. You can also delete by ctrl-clicking or right-clicking on the App and choosing “Delete” from the menu.

Then, I went back through the App Store in iTunes and re-downloaded the applications I just removed. Clicking the “Buy” button on already purchased apps worried me at first, but this support article from Apple said that it wouldn’t recharge, so I went ahead. Sure enough, I got the message “You’ve already purchased this application.” So, no problems there. (FYI: Make sure you check your bank account over the next few days if you do this. While you shouldn’t get recharged, Apple does allow for the possibility of this happening. If you do get charged, contact Apple according the the support article mentioned above.)

Finally, I synced my iPhone again. I did get the error message again, but all the apps were installed anyways. On further syncs, I have not gotten the error message again, so this seems to have solved the issue. Your mileage may vary.