When Charles visits Orry at Christmas, he is a Major. Later, he is a Captain again. At Petersburg, he is a Major and when he leaves, he is a Captain once more.
When Charles visits Augusta for the last time, it is around February 1865 and her pregnancy isn't even visible, but when he arrives short after the war is over (so probably in April or May 1865, See : 2x06
) and finds out she is dead, the baby (born one month earlier) is about 10 months.
Capt. Turner: You think you gonna escape like the others?
Earlier in the war, a large number of Union Officers dug a tunnel under out of Libby prison, one of the largest prison escapes in American history.