We are having the same problem. Screen time limits that are deleted re-appear. I've tried updating all devices to the newest OS that is possible for them, but the problem prevails. I've also tried completely turning off screen time, and re-initializing it and sometimes some random old limits come back, sometimes in duplicate.
Screen time in general is horribly buggy and bad. It is not even clear what the limits mean. What, for example, does it mean if you have two limits on an app, one via the app being part of a category and the other on the app itself. I.e., if I limit specifically minecraft to 1.5 hours but all games to 30 minutes, which limit applies to minecraft? Is it an OR function or an AND function? Searching online only gives endless web pages that often say contradictory things. Apple's own screen time documentation is ambiguous and unspecific. Another thing that is not clear: What is the interaction and priority between the "App limits", "Content & Privacy Restrictions -> Allowed Apps", and "Always Allowed"? It seems that there are in this case three places to say the same thing (e.g., if Safari has an "App limit" to 1 minute, but it is not part of the "Allowed Apps" list but then is "Always Allowed", what is the priority and how are these things combined? It seems right now it is random and dynamically changing based on the direction of the wind).
Overall, Apple has utterly and completely failed in their "ScreenTime" efforts. Steve Jobs would be appalled.