Yeah, in my playthrough she never outright tells you she is pregnant. However, before the metal sign in Ch5, i asked her something like 'something to share?' and she averts it.
And yes, there are many signs:
When she first joins you, Omid says 'should we tell them..?' to which christa says no. Also, when the two of them are talking together by the gas truck, somthing is said like 'safety in numbers', or something that implys that they would be safer in a group
as said, omid's comment of 'cant you see she's-' whilst on the train
When the video is seen of the woman getting pregnant and the sonograph, she is very affected. She throws up at the thought of what the women went through.
she's very maternal with clem. Sure, not a tell-tale sign, but i think it helps.
During ch5, when kenny finds the wiskey, she contempates it for a bit before taking a big swig. Kennys eyes go from her face, to her belly and back again, and his eyes widen. This would suggest that he realises. I think this is why he helps her later.
there are more little references but these are the main ones that i remember