This is the painful part about working jobs where you receive the bulk of your income in relatively few paychecks. You end up grossly overpaying on your taxes because they are essentially assuming that's the amount you receive every paycheck and withhold taxes accordingly. So if you work a boat load of OT every other pay period, and receive like $3k for the first half of a month, and $7k the next pay period, those $7k paychecks are taxed assuming you make $7k * 24 =168k each year, when, in reality you make $120k a year.
There's no good way around this either (to my knowledge). Other than maybe jacking up the number of dependents you have.