Droid 3 stock battery at 30% and wouldn't recharge

I've had my D3 for several months and bought an additional battery and cradle charger with spare battery slot at that time. Everything has been great until yesterday when I noticed that my phone was at 30% charge with the stock battery installed. I swapped in the aftermarket battery, but found that the stock battery didn't want to recharge in the cradle spare battery slot OR in the phone slot with the stock battery installed. The aftermarket battery charges in either location. I put the stock battery back in the phone and connected the USB to a wall outlet adaptor. The phone started to come up in charge level and now that the phone is up to 60%, it will charge when put in the cradle. Did I do wrong by allowing the stock battery to get as low as 30%? I am not a heavy user, no games, limited app usage, but lots of apps installed and I am sure are running in the backround. I generally finish my day with at least 50% charge left, usually more. I had been using Google Maps GPS function on the day in question. Thanks for reading this and I hope I haven't done anything terminal,
Tony AKA Antiqueynot