In sexual relations, Ellie is very inexperienced, she didn't insist on partner using condom. And Larry doesn't use condoms. Ellie doesn't want to be pregnant, but in reality, after such sex with Larry many times, she would, very likely, be pregnant. And Dev. show us Ellie heavily pregnant - it would be right if after this she would become pregnant.
Meh, he's a dumb ass anyway to try to get her pregnant, first Nadia would end his life, second his well off ass would be on the hook for child support. Not to mention if Eugene shows back up in the picture...
He's the only one she is fucking right now, except the one time with his dad, who pulled out. (not in my game though, I shut that scum sucking pig down). I find it hard to think Ellie would do anything for him after catching him peeking at her mom and jerking his dick, so I avoided him.
I find it hard to believe she didn't feel him cum inside her or figure it out later when she went to clean up.
The Dev already showed a pic of her pregnant.
But i doubt very much. Many events of the PB 1 indicate that Eugene may not be Ellie's father. Eugene should require genetic expertise.
This is not the case with a lot of the endings. I'll say it again, this is a story about a father/mother/daughter.
While I can see a slim possibility she is someone else's child. I firmly believe the intent is she is Eugene's daughter.