Perhaps Selene fall head of heels with Michael when he was a Lycan and the fact that he wasn't able to kill him even with Viktor's orders. She protected him when he was a Lycan and kissed him, she had a moment. But didn't even know she turned him?
As for killing Marcus and William...Who the hell would know that?!?! There was nobody else there!!! Heck I would like to know how they left there, I assume they swam :)
At the Coven, Alexander's guys cleaned up the Coven. So no one really knew about where and what happend to Marcus!
Then in this movie (and Awakening) everyone knew about Selene killed 2 elders?!
After Evolution Selene and Michael were on the run. They were not hanging out at a Coven or with Vampire friends.
As for Selene giving birth, perhaps she was only say a month or so pregnant which she probably didn't realize until she was captured, they probably just did a C-section.
Hopefully for the next movie I'd like to see Michael and Eve at the Coven and see everyone's reaction when they see them transform.