The Savings Report includes amortized costs, while the EC2 Instance Cost Report does not include amortized costs.
The difference can be illustrated with costs associated to instances covered by an All Upfront EC2 Savings Plan:
As these Savings Plans are All Upfront (prepaid), there is no monthly commit cost. The EC2 Instance Report does not include amortization, so this will show as $0. Be advised that while it shows no cost, this does not mean those instances covered by the All Upfront EC2 Savings Plan have no cost as they may not be completely covered by the EC2 Savings Plan.