She's talking about his penis.
Mass Effect Comic 'Paramour'
Kelly: We beat the collectors, commander! Isn't it great?
Shepard: Hmm? ...yeah
Kelly: Aww, Why the long face? You're not still pining for Tali, are you?
Shepard: It's just... we're already different species. Why does it matter that I'm a girl?
Kelly: I'm sure you'll find someone, commander. What about Garrus? He seems nice.
Shepard: Already been there. We're completely incompatible
Kelly: Oh come on, you two get along great
Shepard: It's like a claw hammer