Deleted Apps keep re-installing

Still a problem six years later.

Solution: I deleted all the apps from iTunes (select all and Cmd-Delete) and checked to make sure the Mobile Applications in Music/iTunes is empty. You can only delete them from the iTunes library, not from the iPhone device view in iTunes.

So no apps on the computer, and no complaints about missing apps, nor are any apps on the phone deleted when I sync.

"Transfer all purchases from this iPhone" does nothing.

I suspect the problem will reappear if I download any new apps and might have to delete them from iTunes.

Not sure why iTunes keeps a copy of the apps anyway. In case one like Flappy Bird is deleted from the app store? On the rare event that I restore a phone from backup, I can cope with it having to re-download all the apps.

I found a multi-part solution that works for me after trying many others. It is not straightforward, since the solution requires both iTunes and iPhone manipulation. It was a 10 minute fix for me but well worth the invested time: How to Prevent iOS Apps from Reinstalling When You Sync With iTunes

I am having the same issue. I tried unchecking the 'Automatically sync new apps' box, but the problem still occurs. This is very frustrating.

However I have the iOS5 beta, so I can't really complain right now. I hope the issue doesn't persist after the official launch.

It's not an 'issue'... you also need to select the Apps tab and uncheck those apps you don't want on your iPhone.

No, this IS an "issue". Here's why:

1. What's the point of letting me delete an app from my iPhone if this change is not persisted when I next sync? Can you suggest a reason why Apple added a feature to "temporarily delete this app until next sync"? It is clearly a bug. If it's not a bug then it is a very dubious functionality choice.
2. I used to manage my apps using my iPhone exclusively. This included installing, arranging, and deleting. Now I am forced to use my Mac do delete apps. This is a serious usability issue.
3. This never happened to me before. It only started quite recently. Therefore it seems Apple have introduced a major workflow change in the process managing my phone without so much as a popup hint or message. How does this fit in with Apple's whole ethos of simplicity?

At the end of the day I would like to be able to manage my apps using only my device. I would like the iTunes sync to be a 2-way street where changes made on both sides are persisted. I definitely don't want to be forced to uncheck apps using the Apps tab in itunes.

The same thing is happening to me. I can't seem to solve the problem. Everytime I try to sync my phone it starts uploading old apps to my phone. What should I do??