Try starting D:OS EE in the keyboard UI, then in the Controls section of the Options, click the Default button, then Ok and Accept, then go back to the main menu, hit Esc to bring up the key/button prompt screen again, switch to the controller UI, and see if that makes a difference.
Try changing the controller layout used for the game in the Steam Big Picture Mode options.
If you are on Mac:
The latest version of Catalina changed how controller input is being reported. This should be fixable from the GamePadDefinitions.plist file in the app container, which you can manually update. Open the Divinity Original Sin.app container in the install folder, rename the current GamePadDefinitions.plist file (under Resources; see here for the container structure) and copy this version there. This file has been updated for PS3 controllers.