Is your Workspace ONE console version at least 20.01?
Previous versions do not have the "Available OS Updates Sample" under MDM Sample Schedule to automatically check devices for OS versions.
This was a manual query only.
We have the same issue, the console (on Prem) is not reflecting correct details for iOS/iPadOS versions. We run a script that gives iOS/iPadOS versions weekly to us in a report and we noticed quantity didn't match up after updates were sent out (we keep histories of the version quantities). We wrote a script to query all devices every Monday and this has helped tremendously. Sad that we have to do this though.