Has anyone faced any issue while turning off the phantom? When I try to turn-off the phantom by pulling down the sticks together, the phantom just flips over. But if I do it very quickly and precisely then it doesn’t happen.
Is it because I have not calibrated the compass correctly or something? Basically my question is - will phantom try to move or flip over if I press the throttle or pitch sticks “down" while it is grounded or just switched on? I am just starting to use it for the first time and hence not sure about how it works.

If you are going to use the CSC to switch off the motors then as you say, quickly and precisely is the way to go.
Personally I use the throttle down for 3 seconds after landing (or in my case hand catching) as that way you will not tip over.

jonwarr is spot on.  Land,  Hold down throttle until props stop.  They will.   
If your willing to try I would suggest a hand landing with a stearn warning.   Which ever hand you use(Left Or Right) grip the Phantom's rear landing gear midway up the back of the landing gear.

Keep Thumb And Forefinger Horizontal.     
The sudden prop stop can damage not only your finger but has potential for damaging the ESCs.
After the bird is securely gripped,hold throttle down until props stop.
It is easy to forget about the circumference of the props..
Be mindful not to let them rub your forehead...You will know immediately if this happens as you will emit a strange sound.   

johnwarr@live.c Posted at 2015-5-26 02:30
If you are going to use the CSC to switch off the motors then as you say, quickly and precisely is t ...

Is there an alternate way to switch off the motors rather than using the CSC?

The manual shows both ways and I described them above in the post you quoted.

How do you shut of the motors when you have never left the ground? Try to stick your thumb between the running props to turn off the battery?

That's known as the Abu Hamza method, personally I would stick with the same CSC command that you used to start the motors.

Hold stick down for 3 seconds, motors will shut off

When you pull the right and left sticks back the phantom think you want to go down and back and will speed the front motors up that's what causes the flip over. The best way to avoid that is only hold the left stick back and the motors will shut off after 3 sec.

OK, Rewrite the question.
If the motors are started but at idle,
I can only find one way to turn them off. That is to turn off the battery. After a lift off and I land, I use the left stick.
Nevermind, it works, didn't hold it down long enough, thought it would power down quicker since it was at idle.
Probably in a panic mode after trying the two stick method, which has never worked. It actually works better with 4 sticks, sure been eating a lot of popsicles.