Yeah, the whole thing is quite confusing. Here's my take on it:

Cruise's flashbacks: He's imagining his wife having an affair, I don't think they are real scenes at all.

The girl: This one is more complex. Cruise stumbled into something they wished to keep private. Their reaction was to try to scare him into leaving them alone and keeping quiet about it. The girl had a drug problem and ODed, they wove that into the plot to scare him.