You should not have pain. Abdominal muscles can be sore from workout but that's normal and should pass after a day. If you feel the abdominal muscles are hurting STOP training until you have recuperated.
Make sure you have properly warmed-up before sanchin practise (if I am not warmed-up enough I get cramps in my rib muscles).
What bothers me is that you have a sore feeling in the stomach. Check your breathing with your instructor. If the breathing is not correct (abdominal) you should not stress the muscles. If you keep breathing incorrect, stressing the muscles, you will get health problems.
A simple test is to stress the abdominal muscles at virtual maximum and then check your breathing. You should be able to breath in and out without loosing the stress on abdominal muscle. If you feel you can not hold it, or that you are holding your breath to keep the stress, breathing is wrong. In that case, STOP training on your own and seek help from your instructor.