I was having the same problem. It would not let me submit my In app purchases to my app, which I uploaded shortly beforehand. I had to reject the binary, then follow the directions below to add the IAP to the app version before uploading.
- Go to iTunes Connect
- Click on Manage your applications
- Click on the App
- Click “View Details” button
- Scroll down until you see an “In App Purchase” Section
- Add your In App Purchase to that version.
- Then ready your app for upload.
Once these steps are complete, the In App Purchase should automatically change from “Ready to Submit” to “Waiting for Review”.