By smoke and mirrors and stuff buried in the weeds. The POGO blog has a post describing what happened over 20 years ago. To save money, Congress changed the formula for determining hourly wages for CS employees from dividing by 2080 hours in a year to dividing by 2087. (2080 would be 52 weeks in a year, or 364 days in a year. 2087 allows for the 365th and 366th days.) So the change was more accurate, but it had the effect of lowering hourly rates, which would slightly lower budget expenses. The thing is, they've allowed government contractors to use the 2080 figure all along, which POGO objects to.
Nickels and dimes over years add up to real money (although not by Sen. Dirksen's definition).