maybe because the sorting hat saw what was really inside of her. The hat dosen't choose by background. Thats not a way to judge people at all. And she's bellatrix lestrange for crying out loud! the greatest, most loyal, most faithful servant of the dark lord! maybe the hat saw it comming.
2.She always wanted to be in Slytherin, and the Sorting Hat takes your choices into account as it did with Harry Potter.
3.Her whole family has been in Slytherin, with the exception of Sirius Black(Gryffindor).
4.She would be disowned if she was not in Sltherin(The disowned include:Isla Black,Phineas Black,Marius Black,Cedrella Black,Alphard Black,Sirius Black;Godfather of Harry Potter ,and Andromeda Black;Mother of Nymphadora Tonks
I think when they called her to be Sorted the Sorting Hat saw she had indeed most likely become who she is now. I have no clue what happened that night she was sorted but still she was in Slytherin and the hat saw something in her that made it shout Slytherin.