I have APK file, I drop it with mouse to my android emulator, it loads successfully. Then I use following commands to repack APK:
apktool d -s app-debug.apk
cd app-debug
apktool b
I get this error when I drag and drop new APK file. I need -s key to preserve .dex file (I need to replace DEX, but I have same problem when replace) and avoid decompile/compile step:
For me uninstalling previous version of application helped. Using adb from command line helped to identify error message.