Good questions. I was wondering about that as well. Ruby is fully aware of the MC's relation with Emma and likes her. Emma is also more or less aware about the MC's feelings for Ruby (I think, but I also think Emma doesn't know they are fucking). So there shouldn't be that many surprises or too much jealous feelings.
Fair enough, but pulling out is not a reliable way to prevent pregnancy.
So if a girl likes to fuck around while not using contraceptives and/or insisting on condoms, she will need to face the facts at some point.
In several parts I've put the message "xxx will remember this". that doesn't necessarily mean it's something bad, or something that's going to backfire later on. In the future they may make a mention of what they remember, or trigger an event. I guess you'll have to wait for the next chapter to see it.