If you remember at the end of last season, she asked Rick to kill Shane... then when he did, and told her that he killed Shane... she reacted... not as what you would expect when someone asks someone to kill someone and that person actually does what that first someone asked. Wow, hope that made sense.
But yeah, when Rick told her that he had killed Shane... she seemed a little more upset than what one might have expected. If I recall correctly, he even left out Carl's involvement.
So if I were Rick, and that was the way my wife reacted to something she asked for... no, demanded... I might think that perhaps she had more feelings for Shane remaining than I would have hoped.