I don't think there is an issue related to expressing concerns about anything. Communication is important. However, there is an issue in regard to how you expressed it. People are a lot more open to a message when it is expressed without criticism.
I would tend to approach this conversation thusly:
I thought we had all agreed to use protection to prevent pregnancy. I moticed that you two did not use a condom the other night. Did I not understand correctly?
Then I would leave the ball in their court to explain. I would not preach, I would not lecture, I would not criticize. All that does is close communication, which is the opposite of what you are trying to achieve.
As for your primary, he could use a lesson in biology. It takes just one swimmer to reach the egg at the right time. He has no awareness or control over minute amounts of leakage. (I was a biology teacher, btw.)