Baby waking up screaming???

So we recently started a sleep program and its going well. My only issue is my little one is waking from her naps and in the morning crying. She never did this before. Its breaking my heart. I am not leaving her to cry for intervals of time. I stay with her and will pat her back, rub her tummy or sing when she cries, but she does cry when I put her down for sleep. My husband says she is just learning a new routine and she will adjust which sounds reasonable but I'm just so sad. My little girl used to wake up smiling and kicking her feet. Anyone else have this happen when they started a sleep plan or changed nightime routine. I'm still nursing her when she wakes up in the night and offering comfort. The sleep plan was really just to get her in the crib during naps!!!