If he's not taking naps well either, he could have something wrong with his tummy. If that's not the case, you may have started a bad habit. When we adopted our twins--granted, they were almost 3 then--a friend of mine told me this lesson she learned about children's habits. If you do it the first time, they'll wonder if you'll do it again. If you do it the second time, they'll expect it all the time. Her analogy was that if you give a woman flowers once, she'll hope to get them again. If you give her flowers the second time, she'll expect them every time. Your son is now getting old enough to know that his actions can get reactions from others. He's out of the "you can never spoil them too much" stage. That usually ends around six months.
If you think it could be bad dreams, maybe try using music or a white noise machine to soothe him, or a blanket or something to hug. He needs to learn how to soothe himself and go back to sleep on his own, especially since you work and don't have time to nap when he does during the day.