Check the fees summary on your ticket. Do you see any fees for Indonesia? I have a trip coming up ORD-NRT-SIN-DPS-SIN-ICN-ORD, and here's the fees for the ticket:

U.S. Customs User Fee: 5.50
U.S. Immigration User Fee: 7.00
U.S. APHIS User Fee: 5.00
September 11th Security Fee: 2.50
Japan Passenger Security Service Charge: 6.10
Japan Passenger Service Facilities Charge: 12.40
Singapore Passenger Security Service Charge: 9.00
Singapore Aviation Levy: 5.00
Singapore Passenger Service Charge: 23.70
Korea Departure Tax: 9.30

Nothing there for Indonesia. That you pay on departure.