Sure. Yea based on the dialogue Emma did acknowledge that Ian is now with Lena hence she doesn't want to continue her fling with him.Just because Ian wants to cheat on Lena doesn't mean Emma might be automatically okay with fucking Ian when Lena is her friend.
But it could be a bug. I'm not seeing any change in the script which would lead to it. Could you post some specific about when it happens etc?
As to when it happens, it happened on a playthrough where Ian and Lena entered a serious relationship where they agree to experiment with each other. In ch 12 alpha and beta, Ian was able to have sex with Emma during the second day of the beach event (the one where he gets rimmed) and was able to finger her butt while she's lying on the beach. In the final version of ch 12, he can't do it anymore. Hope this helps.