That's why you have two controllers, that way when one is low on batteries, you can use the other one while the low battery controller is charging. As for the issue that you're having, I've encounter that situation in the past. But just kept on trying to charge the controller, and eventually it started working. Then again, could had been something with my usb headset as well, because I had two of them hooked up at the same time along with my controller trying to charge.
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