Question: It seems to be made clear that Holden is the father of the baby, since there were issues with Phil's sperm. However, Justine had sex with Bubba as well. What about the possibility of him being the father?
Question: When Bubba told Justine about the bill for the motel, why did he think she would tell Phil about them? They were never at the motel.
Answer: Bubba was afraid that if Phil confronted Justine about the hotel bill that, not only would she confess about her affair with Holden, but that she might also tell Phil about what happened with Bubba.
Question: Is there any significance to Justine looking almost the same - wearing a jacket over jeans, with her hair tied back - for much of the movie?
Answer: I would say her similar clothing style represents that although she wanted her life to change, it never did, and she ultimately remained stuck in her never-ending routine, always looking the same, never moving forward in a new direction.
Answer: I think you answered your own question. The only certainty is that Phil is NOT the father because of fertility issues, though he apparently deludes himself into believing that he has somehow gotten Justine pregnant.
raywest