It is absolutely normal that you can find yourself between two gears (false neutral) if you don't give a positive push or pull to the shifter. Also, if you don't move the pedal to the end of its travel when shifting - particularly when up shifting - it might slip out of gear, since the dog is not fully engaged. You don't need to be hard on the shifter, just move it all the way up or down when you are shifting.
You can get the feel of this phenomenon easily: Sit on the bike with the engine off, in neutral. Pull the clutch in and the shifter up to second gear. You might need to rock the bike a bit back and forth in order to implement the shift. Let the clutch out and try to move the bike forward or backwards, to make sure that you are in gear. If you are, you'd not be able to roll it more then a few inches. Now, pull the clutch in again and as you keep rocking the bike ever so slightly, start pulling the shifter up as gently as you can, applying force gradually. Here comes the tricky part. You might want to do it with your hand rather than your foot. It is easier to modulate the force this way. When you feel that the shifter moves up - kind of slipping out of gear - STOP right there. Don't pull it all the way up! Clutch out, and see the miracle. If you turn the ignition on, the neutral light will be off, but you'd be able to roll the bike freely. Congratulations, you implemented the task properly and the bike is in false N. This is exactly what happens on the road if you are not moving the shifter positively. There is nothing wrong. This is the nature of this gearbox. Over time, as the gearbox breaks in, the whole shifter mechanism moves around easier and as you also get a better feel of handling, the chances of finding yourself between gears gets slimmer. It does not change the fact however, that if you stop moving the shifter between two gears, you’d be in false neutral.
There is no need for filing, grinding or panicking. Be patient and implement the shifting with a gentle but positive pedal movement. That’s it.
You’ll be impressed by the huge improvement you’ll experience over the first two thousand miles as you proceed with the break in. Shifter gets smoother, bike runs better, quieter, suspension improves, etc. The key again, be patient and gentle. Enjoy the ride!