If you don't push the battery firmly into the charger the balancing pins will not make contact and the battery won't charge. You cannot "top off" an almost full battery with the stock charger, it has to be run down a little before the charger will "see" it as not fully charged.
If you run a battery down to zero, it's over. Dispose of it and buy a new one. Those of you that lack knowledge of Lipo batteries need to, today, Google lipo batteries and learn about them. You treat them right and they will last a long time, Treat them badly and you will buy lots of batteries. Those of you that try to extract every possible second of flight time from your batteries are inflicting significant damage upon them, and that damage is accumulative.
If you are doing everything else right but the charger isn't working for you, call Yuneec. There's nobody here that can fix it for you over the internet. It is possible to have received a defective battery. Again, call Yuneec customer service. That's what they are there for.