The fact that the bike has been run for very few miles from new and then sat for, presumably many months, or at least sat with old fuel in the system, i'm thinking the problem lies in the fuel system, which also includes injectors.
If it's running well at all other times, it might be worth getting some miles on the bike without any stop starts.....just keep that fuel flowing and hopefully it will clean itself up a bit.
As is the case, for many modern engines....If one or more injectors are sticking slightly, that might explain the symptoms here, but then my concern would also be for the catalytic converter, because if an injector is stuck open, it could damage the catalytic converter.
That said, I could imagine you'd be getting some fault codes flashing up on the dash.
Just something to have checked at some point by a trained technician.