I've noticed that in the iTunes/Mobile Application folder there can be multiple copies of an app. I don't think iTunes realized it's the same file just updated and when there is an update for an app it will show "x" amount of updates for "x" copies of that app in that folder.
Multiple copies of the app in the Mobile Applications folder isn't what's causing the problem with multiple update's showing for a single app. I'm getting that problem and I cleared out all the duplicate apps from the folder a day or so ago.
The app update feature hasn't worked properly from day one and it seems to be getting worse rather than better at the moment.