Cost plus percentage gives a very clear incentive to raise costs
Compare the original winning bid for the STS with the actual costs; I think they rose more than tenfold (and the per-flight cost rose more than that), IIRC.
And had the competing team won, the Challenger disaster never would have happened, because the solid-rocket boosters would have been manufactured as units and transported to the Cape by barge rather than having to be broken into small enough components to fit on rail cars.
[1] https://www.nasa.gov/pdf/382045main_19%20-%2020090730.11.STS...