This family tried to keep a confidential lawsuit a secret. Then somebody goofed.

A confidential lawsuit packed with allegations of embezzlement and an unexpected six-figure payment no one knew was due taxpayers are making for turbulent times for one family on the Coconut Grove waterfront.

Sealed court documents obtained by the Miami Herald show that Sonia Lima and her son Alan are accused in civil court of stealing from their Grove Harbour Marina partners, using corporate money to pay their expenses and hiding business that would have increased rent paid to the city if properly documented. The duo, whose family has controlled the property through a city lease since 2003, points the finger back at their accusers: Lima’s daughter and son-in-law, Jessica and Jay Leyva.

It’s unclear exactly how much money is in dispute, as most details of the case have been kept confidential. But shortly before the lawsuit was filed, Grove Harbour Marina and Caribbean Marketplace LLC unexpectedly paid the city more than $100,000 — sparking an ongoing financial investigation by the city.

We thought it was strange that we got a bunch of checks totaling six figures.

Daniel Rotenberg, director of real estate and asset management for the city of Miami

“We thought it was strange that we got a bunch of checks totaling six figures,” said Daniel Rotenberg, the city’s real estate director. “Once we received those checks we went right to the internal auditor.”

The exact details of the case remain sketchy. In an unusual occurrence, attorneys on both sides have successfully petitioned the courts to seal an August complaint and most subsequent motions, citing a judicial rule intended to protect trade secrets, avoid injury to innocent parties and protect “a compelling government interest,” among other sensitive issues.

But a motion that the Leyvas’ attorneys say was incorrectly made public this month states that Alan and Sonia Lima were “determined to divert part of the company’s assets and interests to enrich themselves.” The mother and son, according to the Leyvas, used a maintenance company owned by Alan Lima to perform marina and boatyard services, withhold the money from the family-owned marina operator, and under-report profits and under-pay rent to the city.

Alan and Sonia also used company funds to pay their personal expenses, improperly recorded those payments and falsified or misstated the company’s books and records to conceal their misappropriation.

Motion filed by attorneys for Jay and Jessica Leyva

“Alan and Sonia also used company funds to pay their personal expenses, improperly recorded those payments and falsified or misstated the company’s books and records to conceal their misappropriation,” states the motion, which doesn’t go into details about how much money is involved.

The Limas deny the allegations. They say it was Grove Harbour financial manager Jay Leyva who flubbed the books, alleging that he quietly borrowed money from the company and gave his venture capital firm rent-free space at the complex. The only thing they seem to agree on is that taxpayers were significantly shorted by their company.

“Jay was borrowing money from the company that approached a very high amount of money and had not repaid it. He was helping himself. Alan decided he had to take the finances away from Jay and he did,” said Lima attorney Andy Hall, adding that his client voluntarily paid the city back-rent after two accounting firms reviewed the company’s finances. “We have had the books and records audited twice and everything is paid in full.”

David Pollack, one of Leyva’s attorneys, dismissed Hall’s allegations as standard counterclaims.

“We’re not surprised. That’s a typical defense tactic. We’ve seen nothing to indicate that Leyva was implicated in any of the things you talked about,” Pollack said. “Apart from that, we stand by the portions of the documents you’ve read in the public record and believe that the evidence will bear us out on them.”

Jay was borrowing money from the company. He had not repaid it. He was helping himself

attorney for Alan and Sonia Lima

Rotenberg, the city real estate director, said his office began to look into dealings at the property earlier this year when someone called anonymously to suggest that the city examine the rent received from a Fresh Market grocery store on the property. Shortly after, perhaps just a few weeks later, he said Grove Harbour sent the city a letter along with the unexpected checks explaining that accounting errors had led to underpayment.

Auditor General Ted Guba, whose office found three years ago that the marina was under-performing by about $862,000 a year due to low occupancy rates, declined to comment. The 2014 audit showed that Grove Harbour Marina and Marketplace LLC reported gross annual revenue around $5 million and paid more than $600,000 a year in rent to the city. Monthly rent checks to the city have all exceeded $60,000 since the lawsuit was filed.

The Limas and Leyvas have been players on the city-owned Grove waterfront for decades. They won a city solicitation to develop and operate Grove Harbour Marina back when family patriarch Felix Lima was still alive, and were part of a group of investors who four years ago won control and development rights at the Grove Key property next door.

But the family dispute has bled over to that property as well, where their partners in Grove Bay Investments bought them out in April for an undisclosed sum. Hall, the attorney for the Limas, said the buyout came after Leyva tried to sell Grove Key’s city lease and development agreement to a buyer without first informing his partners and after a dispute arose over a commission he tried to claim on a construction loan.

Grove Bay partner Francesco Balli and an attorney for the company declined to discuss the allegations, as did the attorneys representing Levya in his lawsuit against the Limas.

Leyva is now suing his former Grove Key partners, saying they wrongly terminated a contract held by a company he owns with Alan Lima to manage Grove Key’s operations.