When Booth and Bones are first going to the Amish community they are arguing about the Pope and his 'hat', and Bones says "It's quite ornate for a vow of poverty". Catholic priests do not take a vow of poverty. Brothers and nuns do, but not priests.
The mother of the victim can be seen wearing a wedding band. Amish do not wear jewelry of any kind.
When the parents of the victim watch the recording of Levi playing the piano, framed pictures can be seen hanging on the wall of their home. This is not typical of an Amish home.
As Booth and Brennan are leaving the Amish family house in the final scene one can clearly see a light switch on the front porch of the house. Amish houses do not have electricity.
The character Sarah (Stephanie Turner) is Amish, and so cannot even wear makeup, but in the scene in which she is being interviewed, her ears can clearly be seen to be double-pierced.