No worries...
I've been through four UV-5R radios, and I've seen different behaviors from the chargers LED indicator, but they all did what they were supposed to do. The one that's sitting on my desk right now is green when nothing is inserted, it turns red when a depleted battery is inserted, and it turns green again when charging is complete.
MTS is right, I think - the ChiComm chargers vary.
As long as it's doing it's job, I wouldn't worry too much.