Make sure you don't have any files in Files > Downloads (example Movie.download). They will directly contribute to the Documents/ directory in Safari. Keeping the app closed at night will speed up the process because iOS won't remove data from the apps container directory tmp/ unless the app is closed. Although caches and other temporary files don't contribute to the apps Documents and Data usage plus iOS doesn't zap out the data until it needs it because its just a waste of time, needless wear on the NAND and wasted energy if the space isn't actually needed.
The apps storage usage isn't up to date as you would think due to iCloud syncing and not having data to put in its place.
Quick example. I downloaded a 2 gb file in safari earlier. Safari bloated up to 2.2 gb during the download. The file moved to Downloads in Files/iCloud Drive which went from 2.0gb to 4.7gb, Safari dropped back to 200mb. I moved the file from Downloads on my iMac and deleted the files there, that was couple hours ago and iCloud Drive is still 4.7gb with the Download folder empty even on the iPhone. It does this all the time, I'll ignore it and next time I goto use it it will be 2.7gb again.
Matter of fact my iPad says I have 27.32gb of iCloud space available. My iPhone says I have 22.15gb of iCloud space available. And my iMac says I have 22.55gb of iCloud space available. Syncing this isn't a priority so it doesn't kill the battery making it one.
Once the devices do some storage management on the device it will sync back up again.
Just be patient.