Do you mean that the baby smells sour because he spits out the milk? Why would that happen? Do you mean that the milk smells sour, and the baby gets covered in milk when he spits it out?
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bingo binThe baby smells sour because of the half digest milk was spits out.By "half-digested" I gather that you mean the baby swallowed the milk and later brought it back up. "spit out" doesn't really convey this; you would use another term, such as "throw up", "be sick", "vomit".