Even more late but for anyone else experiencing same, this is exactly what my issue was. Apple had (mistakenly) approved a version of my App and for weeks I was clueless that it wasn't working in production until I submitted a new version which they (correctly) rejected. Everything was fine while testing through xcode over various simulators and real devices so it was WTF for awhile until I stumbled upon this thread. Following the steps in [https://developer.apple.com/documentation/cloudkit/deploying-an-icloud-container-s-schema] hopefully has fixed the issue.

This is one of those "maybe it saves someone else from spending an entire day pulling their hair out like I did" replies for anyone that stumbles in after searching. In my particular case, I have an iOS App, but I often use the "My Mac through Catalyst" simulator function to test it, and although I am not entirely sure what the problem was, I believe the last time I ran simulator I was using that Mac/Catalyst thing before creating an archive and uploading through Xcode, and sure enough it didn't show up on AppStoreConnect, but after way too long of cursing and exasperation I found it in TestFlight under a "macOS" build, not an iOS build where it should be. Simply by running the simulator as an iOS device and then redoing the archive and distribute through Xcode and voila, it appeared in AppStoreConnect Distribution as intended.