You have to unplug the battery or install a switch. Simply turning off the transmitter does not turn off the receiver.
It is very likely that you over discharged your lipo.
Lipo batteries can be ruined if any single cell drops below about 2.9 volts or so. Some chargers will not even attempt to charge a lipo if it detects voltage below 3.0 volts per cell.
You can try to bump the voltage up with a very slow charge but there is a chance you ruined your lipo battery and will need a new one.