Sometimes you just have to remember that people of all sizes have issues with their own body, and something that bothers you with your body can be a bigger or lesser issue with another person who has the same issue. Or, people who would seem to have LESS body issues than you because they're smaller, more athletic, look better in clothes, etc etc actually have more.
Even if you feel like her issue is miniscule compared to your own, you should still be sensitive to it and maybe use it as an excuse to get someone to join you at the gym. Tell her it's not a big deal and she shouldn't worry about it, but if she wants, she can come work out with you so she could lose those 3 extra pounds and get more fit. I wouldn't let her body issues bother you -- I know it's frustrating to hear when our smaller counterparts complain about their bodies, but you have to remember they're human just like we are, and have insecurities just like we do. Treat them as you would treat anyone else with the same issue.
