Why did they stone Achan?
Rashi: He transgressed Shabbos. 1
Radak, citing his father: He needed to be burned (verse 15). When he was taken to be burned, people threw rocks at him amidst great anger at him. After he and his property were burned, they covered them with rocks, and made a rock-pile for a sign.
What did they burn?
Rashi: The tent and the Metaltelim.
What else did they stone (other than Achan)?
Rashi: The ox and the animal(s).