With new iTunes interface a lot of things changed. You can upload your app either from
1) Application loader
2) Direct form Xcode as archive.
After uploading you can chose it from Build section of app detail page in iTunes connect dashboard.
At this moment all things goes in a good way for you. But sometimes you found an unusual bug in your app and rectify it. Now you want to upload this new binary to iTunes. Wait, now your last version is still there on Apple server and when you try to upload the new same version binary it throws an error that they already have same binary with same version.
ERROR ITMS-9000: “Redundant Binary Upload. There already exists a binary upload with build version ‘1.0’ for train ‘1.0’”
Here is the solution for this problem.
1) Open up your project in Xcode.
2) Navigate to General settings page of your app target.
3) Change your Build Version to your version and add .1 to it. Shown inn the image
Now compile it and upload the binary, you will see two binaries for same version there but different build versions. Chose the latest one and submit it for review.