Can I get iTunes to stop updating a specific app?
There is no directly supported way to exclude apps from update. You either can Update All or update one-by-one.

That said, there are a few things you could try. Depending on how many apps are being updated, if it's more than three, the app in question could be queued for download when you click Update All instead of starting immediately. If so, simply remove it from the queue. Similarly, depending on the app's size, it may not download instantaneously so you could cancel the download of it after clicking Update All.

You could use something like Little Snitch to block connections from iTunes, hit Update All, remove the app in question from the list, then reenable connections. Might not work depending on what Update All actually does with network connections. I haven't tested it. If you want to go this route, you could use the answer to this question about the domains for Apple's app CDN to only block the domains which contain the app data, and not control servers which might be used when you click Update All.

Finally, you could try this:


Copy the good version of the app from the iTunes Media folder (usually at ~/iTunes/iTunes Media/Mobile Applications unless you moved either the iTunes or iTunes Media folders) to a safe location like the desktop
Update All in iTunes.
Remove the bad app version from iTunes.
Re-add the good app version from the desktop by dragging it into iTunes.