This is why Bethesda don’t own Lego Corporation. XD

Maybe im just inexperienced at building, but I tried to continue some of the setup they started at the Abernathy farm. I wanted to extend what they did on the upper floor overlooking the tato's and it was slightly elevated so it didnt line up with their placement. I dont know if there is a way to sink the piece into the floor to line it up, but I ccouldnt figure it out.

The other complaint I have is how elevation makes it near impossible to line up fencing so it closes properly from one piece to the next on the last side. I always have to try to seal the last connecting point with a makeshift barrier of poles.

No it’s not you. Many of the building parts - most ? - won’t clip. There are some techniques to work around it. There is a video series called something like No Mods Build School, search for that on YouTube.