Why did ian thomas kill alison?

Because Courtney was certifiably insane. She tried to switch places with Alison. Courtney ditched Naomi and Riley, and then made friends with Aria, Hanna, Emily, and Spencer. Alison got very mad at her, because Courtney was supposed to go to the mental hospital, but since they switched places, Alison went instead. Since they were twins, and nobody knew about it, they thought it was Alison's body in the hole. But it wasn't, it was Courtney's.

Hope that helped!

-A