Derek with Ashley or Wendy is entirely possible. Ashley is naive enough to not protect herself properly. And Wendy and birth control? Why would she need it? It's not every day that some guy HAS to have sex with a feminist.

Tommy with Heather, though, not so much. I think she's too world-wise to get pregnant if she doesn't want to, and I see nothing in the game that would indicate that she is ready for motherhood yet. She's actually quite focused on her studies, and pregnancy would create severe problems in that regard.
Magnar with Sally was another possibility I've considered. It would explain her attitude at the dorm party.
I do believe we can definitively rule out the 5 principal LI's. The pregnancy test is in every possible path. But, the MC doesn't have to have sex, much less cum inside, with any of the 5. And none of those girls is likely to have had sex with any male other than the MC since the start of the game. Sage and Chad haven't had sex for a while at least; Josy is only interested in the MC and Maya; Mays is a lesbian who has never touched a boy; Bella is still waiting for John and only has thoughts about another man IF she is turned on by the MC; Jill is a professional virgin. I know people have come up with theories about all that being lies, but come on... really?
I do think the 'flashback' theory has merit, though. It is exactly the type of thing our beloved developer could throw at us.