I don't see an icon attached?
I've updated Application Loader, XCode, and to the latest version of AGK. I'm still getting the same warning message when I upload my app. See screenshot on ITunes Connect (this is for my Starting 11 Stats app). My app icon is still set to my logo, but you can see the IPA includes an AppGameKit logo. Hence if I submit for review, apple reject it as it has a conflicting logo. So it appears to be an issue with creating the IPA. Can you attach a working logo and I'll try and create the IPA and upload to see if the icon is included in the apps assets?