As U.S. communities ravaged by this year’s series of intense hurricanes and wildfires clear debris and begin to rebuild, many are counting on the federal government to help cover their costs. They could be in for a frustrating surprise.

If history is any guide, some local governments and nonprofit organizations could get less than they were told to expect from the Federal Emergency Management Agency. Others could be asked years from now to repay some or all of the aid they received, if FEMA concludes the projects failed to comply with its voluminous requirements or decides it shouldn’t have approved the payouts in the first place.

Over the past decade, FEMA’s denials and reversals have caused uncertainty and anger in some communities, led to long rounds of appeals, strained local budgets, made it hard for some organizations to stay afloat, and occasionally delayed the rebuilding process.

“My word of advice for everybody is document, document, document,” warned a frustrated Mayor Orlando Lopez of Sweetwater, Fla. “Cross your t’s, dot your i’s and back up everything.”

On Aug. 15, FEMA denied an appeal from the Miami suburb and said it must repay $2 million it received nearly two decades ago to repair storm damage because it failed to adequately document work done. Lopez called FEMA’s actions “completely and utterly unfair.” A few weeks after the denial, Sweetwater suffered a fresh round of damage from Hurricane Irma.

For its part, FEMA is legally obligated to look out for the taxpayers’ money and guard against misuse and fraud by local governments and organizations that overcharge the federal government or use emergency aid to undertake long-desired improvements they couldn’t otherwise afford.

Christopher Logan, FEMA’s public assistance director, said in the agency’s defense that major disasters can result in “extremely complex, technically complicated projects that span many, many years.” But he said the agency has recently taken steps to reduce what he called misunderstandings.

An analysis by The Associated Press found that over the past decade, FEMA headquarters has denied appeals for at least $1.2 billion sought by local governments and nonprofit groups to protect or rebuild communities hit by hurricanes, floods, fires, earthquakes, tornadoes or other major disasters.

The AP reviewed more than 900 final appeal rulings. In one-third of those cases, FEMA granted some or all of the requested funding, totaling about $250 million. Two-thirds of the appeals were rejected, probably totaling well more than the $1.2 billion tallied by the AP because the amounts denied were unclear in FEMA’s online records for more than 100 cases.

The money at stake in those cases was just a tiny fraction of the tens of billions of dollars FEMA paid out during that period. Yet the disputes may offer a glimpse of some of the challenges communities struck by Hurricanes Harvey, Irma, Maria and Nate could face in the years and even decades ahead.

The AP’s review found that FEMA has argued with local governments and nonprofits — and faced disagreements within its own ranks — over hundreds of matters big and small: whether buildings should be repaired or replaced; whether certain damage was caused by a disaster or by pre-existing problems; even whether tree stumps were the proper size to qualify for removal using federal aid.

Among the appeals squelched by FEMA: Florida’s attempt to get $51 million it claimed to have lost by waiving tolls for motorists evacuating from eight hurricanes in 2004 and 2005.

FEMA’s final decisions sometimes come long after a disaster has struck, and even well after the money has been spent.

FEMA officials acknowledge the agency has done a poor job of resolving appeals quickly. In 2014, just 6 percent of appeals to FEMA headquarters were decided within the law’s 90-day requirement. That’s up to 26 percent this year, agency officials said.

Hurricane Katrina alone accounted for one out every seven appeals over the past decade. The storm illustrates how FEMA’s rulings can occasionally be financially devastating to groups and individuals and have long-lasting effects on communities.

“FEMA dropped us like a hot potato,” said Dimitre Blutcher of Harvey, La., former executive director of N’R Peace, a nonprofit organization that helps people with HIV and other sexually transmitted diseases get medical treatment.

Her group’s HIV clinic and main office were devastated by flooding and winds from Katrina in 2005. Days after the storm, she said, FEMA asked her to continue providing services to clients. FEMA paid the group $105,600 for its work, which included the long process of reconstructing clients’ files after the paper records were destroyed.

Blutcher said FEMA and state officials led her to believe the clinic would qualify for additional money, so she took out a bank loan and line of credit while awaiting reimbursement for her costs, which grew to $280,000.

But FEMA reversed course in 2011, saying it would not provide any more reimbursement and ordering the group to repay the initial $105,600, too. The clinic soon closed.

“They didn’t care that they promised us the money and we spent it. They didn’t care that I took out a line of credit to keep services going,” Blutcher said.