Battery charging indicator and USB has, sort of, stopped working on my Samsung Google Nexus I9250
Did you try a different battery? Is this one the factory one? It may be faulty and possibly not charging reliably.
If worst comes to worst, you can try reflashing your GNexus with the default google 4.3 yakju images (after backing up all your data of course) to see if the problem goes away. If it does not then the battery needs to be replaced. 


Here is a link: https://developers.google.com/android/nexus/images#yakju 
and information on how to do it: tutorial
You will need to have fastboot and adb installed. 
There is a way to flash the images without erasing the userdata/sdcard partition if you don't want to backup. (it involves editing the flashall.sh to remove the -w option before running it)