Maybe this will help someone - I had the same issue with System Data being over 50Gb on my iPad. And the culprit was actually a messaging app, Telegram, that had no limits set for storing media. It was so much clogged that I was unable to clear cache in-app, it would get stuck estimating the size.
In short, I have uninstalled the app, restarted iPad, installed the app and set the storage limits (cache was empty after uninstall). Then went into iPad storage options and was able to see how System Data is gradually decreasing from over 50Gb to around 10Gb.
So, if anyone is having similar issue it is probably some rogue/broken app that fills System Data with trash.