A 24-year-old Fremont man was bewildered when four police officers came to his front door on a Saturday morning in September, saying they had a warrant for his arrest.

The man, a teacher’s assistant and college student who lives with his parents, was taken to jail in gym shorts, and spent a day behind bars. He was released after his father posted bail of $1,500.

He found out later that he was arrested on an invalid warrant — and should never have spent time in jail. The problem, officials say, lies in the county’s new digital case management system. The warrant had been issued in July for failure to appear in court to dismiss a previous drug possession charge, but the warrant was subsequently tossed out by a judge. Yet that decision never got reflected in the court’s new computer system, which continued to show the warrant as active.

“It’s affected my relationship with my parents,” said the man, who spoke on condition that his name not be used. “They’re not going to believe that four cops came to the door and messed up. It’s affected my relationship with my neighbors, because I’m assuming everybody saw.”

He’s among dozens of people whose lives were jolted after the county began using a new software system, called Odyssey, that Public Defender Brendon Woods says has led to his clients’ civil liberties being trampled. Four months after its launch, there have been wrongful arrests and imprisonments, Woods says, and a testy battle between the public defender’s office and court administrators. Woods wants to see the system fixed immediately, or tossed, but some officials say it’s too early to give up on a system that cost $4.5 million in public funds.

Debbi Pearson, who heads the Alameda County courts’ local chapter of the Service Employees International Union, said many of the problems stem from Odyssey’s cumbersome user interface.

“With the old system, it took maybe one or two clicks to complete a process,” she said. “Now it takes 25 clicks, and there are drop-down boxes and all of that.”

Because the system is so unwieldy, clerks are unable to enter data in the courtroom, she said, so that burden has fallen on other office workers. It’s created a backlog of more than 12,000 files that have not been uploaded — and that number is growing by up to 300 files a day, according to Woods.

Odyssey, which is made by the Texas-based company Tyler Technologies Inc., was purchased to propel Alameda County’s courts — and 25 other court systems throughout the state — into the 21st century, replacing paper files with a streamlined, searchable database.

A spokesman for Tyler declined to comment on the specifics of the Alameda County court system, but said the company “is fully supportive of our clients and we work to resolve any system issues directly with them.”

“We have reiterated our commitment to that approach to Alameda,” he said.

The software first caught on in 2012, after the state abandoned a disastrous $500 million project to develop a system for all of California’s 58 trial courts. Two years later, the state enacted a law that severely limited the amount of money courts could squirrel away, and many courts went on one-time spending binges to avoid giving their reserves back to the state, said Alameda County’s Court Executive Officer Chad Finke, who manages the courts’ budgets. As a result, many signed contracts for Odyssey software, Finke said.

“Tyler sold Odyssey as being an off-the-shelf, easily configurable system,” Finke said, noting that the court purchased Odyssey as a replacement for its 40-year-old criminal records database.

Now he’s dealing with daily complaints from the public defender’s office.

On Nov. 15, Woods filed a motion in Alameda County Superior Court, demanding that the county give up the new software “until the many problems can be fixed.” The court scheduled a hearing for Jan. 17, which Woods said will be too late for defendants who would face extra jail time due to backlogs or errors. He plans to file an appeal in a higher court.

In his motion, the public defender described how the system had disrupted dozens of lives, causing bench warrants to be issued erroneously, misdemeanor convictions to show up on rap sheets as felonies, and defendants to spend a total of 130 extra days in jail. In two particularly unsettling cases, an Odyssey glitch caused two drug defendants to be tagged as sex offenders, Woods said.

“I don’t quibble with the court’s decision to purchase an upgraded system,” Woods said. “But I think this system is terrible.”

Finke acknowledged there are problems with data entry.

“It’s a system where in order to input a judge’s ruling, you have to pull down multiple tabs and wait for load times,” Finke said. “Even our best clerks have a difficult time keeping up.”

The problems have been so crippling in Alameda County that court officials opted not to use Odyssey for family, probate or civil cases. Finke said that other courts with Odyssey contracts have pushed their “go-live” dates back.

“If there’s a silver lining, it’s that maybe some other counties have learned from our experience,” he said.

Even so, officials at California’s Judicial Council — the body that sets policies for all the state’s courts — are sanguine about the product.

Speaking at a Nov. 14 meeting of the council’s technology committee, Chief Information Officer Robert Oyung encouraged the courts to expect “growing pains” as they rolled out the new system and “set their expectations appropriately.”

He said the 26 courts with Odyssey contracts have formed their own technology workshop, the California Tyler User Group, to tackle software challenges. So far, they have logged 52 issues. Clerks in several counties have run into trouble trying to file written minutes from a court session, Oyung said.

Nonetheless, Oyung was optimistic that the problems will soon be fixed.

Finke, too, is hopeful. In addition to spending $4.5 million for the contract, the county’s various criminal justice departments — including the sheriff’s office, the public defender, the district attorney, the probation department and Santa Rita Jail — spent months linking in to a common database that supports Odyssey, he said. He doesn’t want to see that work go to waste.

“We’ve expended the money, and we’re engaged in some internal work that I think is going to help with a lot of the issues Brendon has raised,” Finke said. He added: “We’re not ready to abandon this ship yet.”

Rachel Swan is a San Francisco Chronicle staff writer. Email: rswan@sfchronicle.com Twitter: @rachelswan