Was the battery dead to begin with? I've had the same thing happen to me. When I leave my V3 for a long period of time with a dead battery in it, it starts to make a high pitched beep until I take the battery out. It's normal, and causes no harm to the system, so don't worry.
When the battery is dead, and you dont change it for a while, the tamagotchi mkes a beeeping noise to let you know. I'm 100% positive its normal. hopei helped!