After 21 years in the military, three deployments, and a roadside bomb blast that left him bleeding and unconscious, Christopher Van Meter got a letter from the Pentagon saying he improperly received enlistment bonuses and now owed the government $46,000.

“I was having to choose between buying diapers and food for my children and paying this debt,” said Mr. Van Meter, 42, a former Army captain who now teaches high school near Modesto, Calif. “I spent years of my life deployed, missed out on birthdays and deaths in the family, got blown up. It’s hard to hear after that that they say I haven’t fulfilled my contract.”

Mr. Van Meter is one of nearly 10,000 National Guard troops in California who have been ordered to repay re-enlistment bonuses and other incentives doled out during the wars in Iraq and Afghanistan after an audit in 2011 uncovered widespread fraud, mismanagement and overpayment by the Guard in the state.

Some of the troops have been trying unsuccessfully for years to get out from under the debt and many are struggling to repay it. The Los Angeles Times, which first reported on the impact on troops, found years of appeals had not brought relief. Requests for help from Congress by the Guard’s command went unanswered. Mr. Van Meter had to roll the debt into his mortgage to make ends meet. Others have ruined credit and face stiff penalties for missing payments.