I'm going through the same thing! I have a little girl, Maia, and she's 12 weeks. When we last had her to the vet she was 10.5 lbs. at 10 weeks. I thought the lack of weight was because she was an easy-going pup and her sisters (much bigger than her) would get more food. After a two weeks with us, she's gained. Then sometimes I'll look at her and she'll look so thin and then other times she'll look a bit more filled out. I think it's just a strange period because she's growing so quickly. (She'll wake up sometimes and she'll look bigger, if that's possible.) I worry, but then look at how happy she is and at how shiny her coat is and that usually mkes me feel better. Being concerned is just part of having a puppy.
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Proud Parent of Maia, a honey brindle with four white socks and white neck and nose