Hmm, it really shouldn't hurt...that said, you DID just give birth, so your core will be weaker than usual, and babywearing mostly works your core muscles. If it was general soreness, I'd guess that you just need to strengthen your babywearing muscles a little. But since it sounds like a more localized pain, I wonder if something else is going on. You might want to check where your shoulder straps are placed on your shoulders. I find that when they're too close to my neck, it hurts my neck. Also make sure the carrier is tied tightly enough that your baby's weight is pressed securely against your torso...if you lean forward, she shouldn't have enough room to fall away from you into the carrier, she should stay in place. If she's not pressed snugly against your body, her weight will drag down on your shoulders and upper back and can make you ache. I'd also pay attention to your posture while you're wearing her. I know that my posture was awful for months and months postpartum, and I really had to focus to not slouch or slump, especially while babywearing.
If you post a picture of yourself wearing her in the mei tai, I can check it to make sure there's nothing obvious that needs tweaking.