I've been creating my own underground military compound for my faction, everything is going good;
The entrance is in the ruins of the white house. Which, IMO makes it instantly four times better.

I decided to change the ruins of the white house (The part the player transports to, with the skeletons, fatman, ect).

I removed all the rubble from inside the building, haven't touched outside the building (Pillars, basemant walls, ect) Just removed the rubble, skeletons, fatman, and the radiation marker.
I added in a chain link fence and a utility door. and Changed the texture on the ground to wasteland asphalt (Or something along those lines.)

I go to load it up to see how it works;
It crashes every time I try and load a save while I'm using my mod plugin.
I've tested the game with the plugin unselected, and it works smoothly.

I know this is a pretty broad question, but I was wondering if anyone has the slightest Idea of what is wrong.
Also; im running the unpatched fallout 3; I have every addon except the Pitt and Mothership zeta (Never really liked those on the xbox version) but im not using any patches

1. You should have the game and geck fully patched.
2. Deleting vanilla objects is usually a good way to crash the game. Either make them initially disabled, or move them below the ground.