When I open the pip-boy map, there's this pulsing box on Abernathy. It's not a solid box, only outline.

I go there, there's never anything. Farm is OK, resources OK, no enemies.

How do I get rid of this marker?

sounds like a maker you place on your own and it sounds like you placed it on accident. click any where on your pipboy map and it will ask you if you want to mark the area or remove your marker. This should fix the issue.

Forgive me if im wrong here but it sounds like you put a marker there. Just go the map in ur pipboy, click an open spot on the map and select remove marker.

Edit ^^What he said

IIRC, I had a similar marker when I got an alert for an attack at Abernathy Farm. Stick around awhile. I never saw the (living) Ferals, but that was mostly because of the Turrents I placed.