Plot hole: The rape scene in the parking lot... there is no one around for THAT long? But wait, once the detectives come in the scene two people are walking in the background with a shopping cart - they must have seen something!
Plot hole: One scene we are in the alien's (when she is still normal) living space and we can hear through a speaker everything the scientist is saying...wouldn't the alien pick up that something was happening and do something before...?
Answer: She was most likely giving herself a breast-self examination. Doing this would enable her to feel for lumps, distortion or swelling which if felt early would mean that she might have early stages of breast cancer and could get it checked immediately.
Her breast was sensitive and painful because she could sense that something wasn't right with her.
So the alien embryo inside of her body was giving her cancer?
No. It wasn't giving her cancer. She probably does a breast-self examination periodically to insure that there's nothing wrong with her breasts.
Plus, it wouldn't make any sense for an alien embryo to give her cancer since after giving birth to an alien hybrid she would immediately die.