Auto-instrumentation generates a working folder (with the name of the APK file) at the location of the provided APK file and stores the result in the dist folder. The path to this folder will be <pathToYourApk>/<nameOfAPK>/dist/.
There are three APK files in this folder:
I am guessing you are uploading the final.apk file (Option 3 above) with the Dynatrace debug certificate.
To upload your mobile app on Google Play, you have to sign the instrumented APK <pathToYourApk>/<nameOfAPK>/dist/<nameOfAPK>.apk (Option 1 above) with your Google Play certificate. The auto-instrumentation script does not automatically sign the instrumented APK file with your Google Play certificate. Therefore, you have to do this step manually. First, you have to zipalign the APK file and then you have to use the tool apksigner to sign the APK file with your Google Play certificate.
Go to link and scroll to the bottom of page for more info (This applies to auto instrumentation from the command line)
Hope This Helps