J.B.
It's very common at this age. My SD is petite and in great shape from year-round martial arts (she's 14, 5'3", 115 lbs, size 0 or 2) and even she was self-conscious about her body for a few years. When she was 11/12 she went through a phase when she dressed like a homeless man - oversize plaid flannel shirts, very picky about pants and shorts, etc. She was a strikingly pretty girl who dressed hideously. I think that at that age it was about hiding breast development and curves - she just wasn't comfortable with starting to look like a woman instead of an child. Some of my friends' daughters would wear three tank tops instead of a bra as their own form of denial about growing up. Others had girls in baggy clothes year round.
All I can say is that they all seemed to outgrow this phase. By 7th grade, these girls started to show an interest in fashion and were able to wear flattering (even feminine!) clothes more easily. My SD still has some hangups about things but slowly she's starting to take some risks and wear cute, funky things again. In a couple of years, most of her peers will have caught up in terms of size and development. In the meantime, try to not make a big deal out of it - she's got a lot of changes ahead of her in the next couple of years and the only way through it, is through it.
ETA: If she doesn't do a sport or something physical like dance, try to find a physical outlet that she will enjoy. My SD never did dance or played a team sport (which is a shame) but she completed her black belt in Karate a couple of years ago. Since then, she's been doing kickboxing and even traditional boxing regularly at a local boxing gym and I think that not only is it great exercise, but doing something where a girl can see her own strength and coordination grow is very empowering and can make her appreciate the power of her own body and see it as a source of strength, not something to be ashamed of or hide. If she doesn't do anything regularly now, see what she's interested in or find something for the two of you to do together (even yoga or Zumba). If she can start something with a friend, even better!