You can send a copy of the file to the Documents app from other apps using the Open in dialogue (please note: only files can be exported to Documents; notes or web pages cannot be shared to Documents, they need to be converted to files first).
If the Documents 6 app is not among available apps, please make sure the latest iOS version is in use on your device since the performance of extensions relies on the system.
If updating the iOS does not help, you can also scroll the list of apps until you see the More button, tap it, then drag the Documents app to the top of the list, disable toggles of apps you do not need in the Open in dialogue, restart the device and check the situation after that.
You can also save files to a specific folder in the Documents app (e.g. when saving the PDF file from Safari) using the Files app. For this follow the steps below:
Note: if Documents is not in the list of extensions in the Files app, open the Files app > 'Browse' view, tap 'Edit' in the top right corner, enable Documents toggle in the list of Locations, tap 'Done'. Now you will have access to the local files and folders in Documents via the Files app.