A common mistake is to shoot with your head to the side of your opponent, at or just above his hip level. That puts it in a position where it's easy for him to counter with that choke. If you find you are doing this, you can shoot with your head driving into his abdomen area in front of him, instead of just placing it to his side. Use your head, so to speak...
Alternatively, shoot lower, or even place your head higher. If you can, try a shoot on someone where you can see your own position in a mirror, or on video if you have access to one where you train. You're probably making it easy for the guy to counter, and a little adjustment of your head placement will take most of that opportunity from him.
Hope that helps,