Are you also using them correctly via pinMode(pin, INPUT_PULLUP) (or INPUT_PULLDOWN)?
How does your code look?
You can always add external stronger pull-resistors.
That is a normal behaviour due to limiting the max charge voltage for safety reasons.
You could lift that limit slightly if you want to take the risk and can make sure that the temperature won't exceede 45°C.
See here Electron Charging? - #39 by ScruffR
System.reset() would be the obscure call