Hey there yogini!!!
Hmmmmm… I never like to use the word ‘hurt’. It is so subjective. And everyone has a different pain threshold, so what doesn’t ‘hurt’ someone, may cause damage in another.
Probably not in this particular case. What your teacher is trying to have you do is activate your abdominal muscles.
Because your diaphragm works on the inhales, during your exhales you are trying to expel the air up and out with that short, sharp, forceful abdo compression. You may feel toward the end of repeatedly sucking in your tummy that you feel some muscle fatigue (sometimes like a cramp). This is probably what your instructor is referring to.
On the technique side:
It is possible to exhale repeatedly without really engaging your abdominal muscles. In fact you could stick your belly out and do this pose, and it obviously wouldn’t get you the same results. 
You are probably just going to have to get super-conscious about this for a while until you ‘get’ it. Forgive me if you already have it handled and you are just concerned that you just don’t feel the ‘hurt’. It probably is worth mentioning that you could focus your visual attention on your belly during this pose. Lift your yoga top if you have to, to watch your muscles activate. And/or you could place a palm on your tummy and FEEL the activation. Your muscular effort will surely increase over time as you learn the finer distinctions.
As long as you see and feel your abdominal muscles contract in and up to expel the air, you have the basics. Take it from there!
Namaste
Gabrielle 
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