The question is - are these spots a discoloration of the stem or raised, brown, bumpy areas? I'm not familiar with any disorder that causes brown spots per se on the stem. If raised areas, it could possibly be scale insects. They look like hard shells and are approximately 1/16 to 1/8th inch in size. You should see a sticky material or honeydew in association with them and you should be able to scrape them off. If it is scale, treatment is a challenge to be sure and kill the hatching eggs. Therefore, several treatments are usually needed. If you think you have scale, check with a local garden center/greenhouse for recommended controls for your state or contact a local extension office.