My son was diagnosed with ms in april he tonight says that he is having a very strong pain between his arm pit and his waist can that be a muscle?

Not likely: Ms patients encounter pain not infrequently and the incidence is about 60-90%, based on surveys. The pain could, in this case represent a spinal cord relapse and does need attention, as most relapses can completely reverse with timely treatment. You do not mention his disease modifying agent; this may need reassessment, as better control achieved with tysabri, (natalizumab) gilenya, tecfidera.