I had similar issues with the new Transporter app and a pipeline using fastlane to upload, both giving no errors and a successfull upload statement.
For some reason the app did not show in App Store Connect, under activity or anywhere else for that matter, tried upload again and the error with the duplicate build number appeard (appearently Apple had the binary).
Bumped build number, build again. Uploaded again after 3 days, same issue. As it has normaly only taken 10 min or so before the app has been available i tried again a couple of times at an hour intervall or so, same result but with a slight twist for one of the builds for some short time the app did show up in the "Activity" tab with a an error message "Invalid build". And after some time I also got an e-mail from apple stating that I was missing a purpose string in the Info.plist file.
To conclude ther seems like there is an issue if the app failes and you do not have uploaded an app with the same version number before they dissapear and if there is an issue with the e-mail delivery the developer is left in the blind until he just tries to upload again and again until it works.