I’ve had this ongoing issue where iTunes says I have 3 app updates available after I update all apps and it’s been happening for over a year! I did some research and the first solution was to sign out of my account and sign back in. Sign out = nothing shown. Sign in again = 3 updates available still shown!
Finally I realized what the problem was. I spent some time abroad and when I was abroad I entered my foreign address as my point of contact. So even though I have 1 iTunes account… it was active in 2 locations and some apps are location based. After deleting the three apps I purchased when abroad the problem went away!
I got tired of going through my e-mails to figure out what apps I bought, so in the end I just deleted all apps and then synced my phone and transfer ed apps from my phone to iTunes. I figure if I use the apps again that I’m not currently using, iTunes will let me download them for free since I already paid for them.