Hello @antimix
I see the same on my M5Stack (Gray) - when I turn it off manually I still measure about 2 V on the Groove port.
In contrast when I do the same with an M5Core2 the Groove port is properly turned off when M5Core2 is turned off.
Since there is no full schematic for the M5Stack (Gray) it's hard to tell why the Groove port isn't fully turned off and if there is a way to really turn it off.
BTW: even with the Groove port not fully turned off the battery should not have been depleted completely as the battery has a built-in protection circuit which in theory should prevent under- or overvoltage.
Thanks
Felix