I finally figured out that there is a bug in the NDK, following the steps in this article link
To be able to set breakpoints I had to only build only one version of the shared libraries to avoid the linker from choosing the wrong shared library. Basically I had to change the file Application.mk with the following:
APP_ABI := armeabi armeabi-v7a APP_ABI := armeabi #armeabi-v7aNow I can continue using breakpoints within the android NDK.