You might be using an older version of the Android Gradle Plugin. Plugin version 8.5.1 and above can build APKs properly with 16KB native libraries, but you need version 8.5 to properly build the bundles (aab files), so perhaps the APK you were testing with was fine but the AAB you were uploading to Google Play wasn't.

https://developer.android.com/guide/practices/page-sizes#agp_version_851_or_higher