We also have the same issue where appA uploaded with Fastlane to TestFlight seems to have been associated with appB and vice versa and we get emails from TestFlight saying build was rejected

Same issue for us. Apps uploading according to Fastlane but not appearing in TestFlight or just stuck in "Awaiting Upload"

Yes we have the same issue in 2025. It's really affecting our productivity since we have tons of apps which we upload to testflight with fastlane and some just never show up.