Same here. I upload the first binary for a new app I made, but in app store connect it still says 'Upload your builds using one of several tools. See Upload Tools'. If I try again from Xcode I get the error about duplicate version. I had no issues uploading binaries for another app in the past.

[SOLUTION] I finally figured it out: turns out even though Xcode says the upload was successful, the upload might still fail some checks from Apple. The only place to see those failures is in your email inbox. Apple sent an email to the email address of the Apple developer account I was uploading to and it had the errors that prevented the binary to be available in App Connect. The title of the email is "App Store Connect: Your app "..........." has one or more issues". Make sure you check the various emails associated to your developer account.