You are not alone. In fact, it seems to be a deliberate move on Apple’s behalf. Why? I don’t know. It used to be that no matter how you updated your apps — whether it was via iTunes on your computer or the App store on your iDevice — the apps would then automatically update on all your machines the next time you initiated a sync.
It’s not that way anymore.
Now, if you update an app on your iDevice, it will NOT move over to your computer. iTunes will still show this icon, telling you that you need to update your apps, even if you’ve already done so on your iDevice and synced everything.
If you update your apps on your computer first, then sync with your iDevice, everything will work like it should. But I’m guessing that you — like everyone else on the planet — are manually syncing up your devices less and less frequently, if at all. (Though I highly recommend that all iPhone/iPad owners sync up their devices occasionally at least for safety/back-up purposes.)
So how do you get your updated apps over to iTunes without redownloading them all again? Simple. First, if you’re using the latest version of iTunes and no longer see the handy “sidebar” that looks like this…
…you can bring it back just by going to the VIEW menu at the top of the screen and selecting “SHOW SIDEBAR.”
Then, with the sidebar back — and really, why wouldn’t you want it back? it’s great! — all you have to do is right click on your iDevice and select “TRANSFER PURCHASES.” (If your mouse/trackpad can’t “right click” then hitting the control button when you click will bring up the same little menu.)
This will make sure that everything acquired from the App store on your iDevice — including updated versions of Apps — is moved over to your computer. That’s it.
If you’ve downloaded a lot of app updates on your device and don’t want to download them all over again on your computer, that’s all you have to do. This is handy if you’re on a data cap and only want to download apps once for all your devices (using the computer to sync them all up). It’s also a handy way to just make that darned “you’ve got 28 apps to update” reminder go away.
Here’s hoping that a future version of iTunes restores the ability to do this automatically with every sync.
UPDATE: The newest iTunes 11.0.5 now syncs updated apps both ways! The above steps are still handy for getting music and other content off the phone, though.