Maybe you installed the F-Droid version and want to update with an APK from GitHub or vice versa? Android does not allow app upgrades when the signing keys differ. This ensures the original developer has condoned the app.
This means, you need to either get the APK from the same source, or backup your NewPipe database, uninstall and reinstall the new app. Without a backup, current app data is lost, including subscriptions, history, playlists and settings. Follow this tutorial to do so.
The final solution to this problem is to have reproducible builds for NewPipe in F-Droid. We are working on this with the F-Droid developers here.