EDIT: The answer by Pang is actually correct https://stackoverflow.com/a/28759797/1436766. I will keep this answer as it did resolve a similar problem.
I was facing the same issue today. I uploaded my apk, and the console told me the apk had a Native platform 'joda-convert-1.5.jar'. Surprisingly I was not using that jar anywhere directly. After researching I found out that the jar was being used by another library I was using. And it was in the 'lib' folder of that jar. Since I had the source code of that library, I recompiled that library by placing that 'joda-convert-1.5.jar' in the 'libs' folder. And cleaned and recompiled my app. Everything was fixed.
It seems that anything in a 'lib' folder is seen as a Native Library, and hence the developer console shows it like that. Make sure the libraries are in the 'libs' folder.
Hope this helps.