So, Ellie's worst fear is ending up alone, in the form of loved ones dying or leaving her. Soooo, yeah, she's gonna see a lot of dead and retreating Joels around the place, since he's the person left that she truly cares about. (I might take it further and have her believe the entire place is completely desolate until someone approaches her/talks to her. If that's allowed. idk)

There's also David, a cannibalistic killer who kidnapped her and who she ended up murdering. She is afraid of him, but that fear has mostly also transformed into pure anger and rage. Thus if she sees him, she might lash out and attack him. So if anyone wants to see a teenager totally stabbing the shit out of... nothing, look no further.

To a degree she is scared of the infected from her universe. But that fear is nothing compared to the above - especially the 'being left alone' thing. So, those creatures might just come up as reasons Joel died or something.