After the end of the game I accidently left her on top of the tower I finished the game with the min men. Now when I attempt to go back to the top of the tower it bugs out and I fall to my death.

Ride a vertibird up to the top or fast travel.
Mass Fusion Exec Suite.

That elevator never went all the way up for me either, only down.

I never joined the brotherhood

I didn't join the brotherhood