Because that's how these things work. Why should anyone have to work for the Feds for free? Google, Yahoo, Apple, Microsoft, AT&T, Verizon, Sprint, T-Mobile, etc etc all get paid for costs incurred to aide law enforcement. It's actually a tidy little business.
Also, $3,500 isn't worth discussing. The hearing to deny the motion cost more than the money involved. The Feds simply wanted access to more data than they were wanting to officially claim.