I submitted a new version of my app Pomodoro Tracker yesterday, adding support for Apple Watch. I encountered several issues when submitting the app, just list them below.
1.Version and Build Number
Make sure the version and build numbers for your iPhone app, WatchKit extension, and WatchKit app are the same in the binary you upload.
2.No matching provisioning profiles found for WatchKit extension
I found the answer on stackoverflow
You need to create two new AppIDs in the Developer Portal with the correct bundle identifier for your Watchkit app and Watchkit extension. The bundle identifier has to extend the main apps identifier, so if your app is com.myapp it should be com.myapp.watchkitextension and com.myapp.watchkitapp. You also need to create the related Provisioning Profiles for the AppIDs, one for the Watchkit extension and one for the Watchkit app.
3.Invalid Icon - The watch application 'Pomodoro.app/PlugIns/Pomodoro WatchKit Extension.appex/Pomodoro WatchKit App.app' contains an icon file 'Pomodoro.app/PlugIns/Pomodoro WatchKit Extension.appex/Pomodoro WatchKit App.app/AppIcon29x29@2x.png' with an alpha channel. Icons should not have an alpha channel.
You just need to re-export the icons in Preview, but uncheck the Alpha checkbox when saving.
Hope this helps,