Three tubs of absentee ballots that never reached voters were discovered in a postal center outside Milwaukee. At least 9,000 absentee ballots requested by voters were never sent, and others recorded as sent were never received. Even when voters did return their completed ballots in the mail, thousands were postmarked too late to count — or not at all.

Cracks in Wisconsin’s vote-by-mail operation are now emerging after the state’s scramble to expand that effort on the fly for voters who feared going to the polls in Tuesday’s elections. The takeaways — that the election network and the Postal Service were pushed to the brink of their capabilities, and that mistakes were clearly made — are instructive for other states if they choose to broaden vote-by-mail methods without sufficient time, money and planning.

More than 860,000 completed absentee ballots had been returned by Tuesday, already a record for Wisconsin spring elections. But for thousands of other voters, who never received their ballots, there was only one recourse: putting their health at risk and defying a stay-at-home order to vote in person during the coronavirus pandemic. Many chose not to show up.

Federal health officials have suggested that expanding voting by mail could help reduce crowds at polling places and therefore make elections safer amid the outbreak. The issues that have arisen in Wisconsin offer a warning for other states of the potential pitfalls of a rapid, last-minute expansion of absentee balloting, particularly one marred by a flurry of court challenges and 11th-hour rulings that created confusion and chaos.

The mix of missing and mismarked ballots suggests that thousands of Wisconsin voters were effectively disenfranchised, an issue that Justice Ruth Bader Ginsburg warned of in her dissent to a Supreme Court decision on Monday that blocked extended absentee balloting in the state. Tens of thousands of people who did not receive their ballots in time, Justice Ginsburg wrote, “will be left quite literally without a vote.”

But many Republicans, and even some Democrats, have continued to cast concerns on the security and veracity of vote-by-mail systems, especially ones expanded so rapidly.

“It’s a harder system to administer, and obviously it’s a harder system to police writ large,” Gov. Andrew M. Cuomo, Democrat of New York, said in a radio interview on Thursday, when asked about the downsides to expanding voting by mail. “People showing up, people actually showing ID, is still the easiest system to assure total integrity.”

In Wisconsin, the missing votes could also portend a long legal battle over the results; one race on Tuesday’s ballot was a hotly contested State Supreme Court seat that, in a normal election, was expected to be extremely close. The margin in the state’s 2019 Supreme Court race was about 6,000 votes.

“This has all the makings of a Florida 2000 if we have a close race,” said Gordon Hintz, the Democratic minority leader in the Wisconsin State Assembly. Mr. Hintz, who lives in Oshkosh, was one of the voters who never received his absentee ballot — even though the state’s website said it had been mailed to him. He chose not to vote in person.

Others in Mr. Hintz’s district may have encountered the same problem. On Tuesday, calls began flooding the office of Dan Feyen, the state senator whose district includes Oshkosh, from voters saying they never received their ballots, even though they were told their ballots had been sent out. Nearly every one of those voters had requested their ballots on one of three dates: March 18, March 22 and March 23, more than two weeks before the election.

Mr. Feyen, a Republican, filed a complaint with the Wisconsin Elections Commission, asking it to investigate. He also wants those voters to be given a chance to fill out and return ballots.

On Wednesday, the commission received a phone call from a postal worker in Milwaukee who said three bins of absentee ballots had been located that had never reached their destinations, mostly in Oshkosh and nearby Appleton. The number of ballots in the bins was not clear.

A spokeswoman for the Postal Service, Martha Johnson, said Thursday that officials were “aware of potential issues with absentee ballots in Wisconsin and are currently conducting an investigation into the claims.”

Meagan Wolfe, the elections commission’s administrator, said she did not think the U.S. Supreme Court decision left any room for ballots to be counted if they were not postmarked by Tuesday’s deadline. “There really isn’t any additional things for this election that a voter could do if their ballot didn’t make it by the deadline,” she said in a news conference on Wednesday.

Many of the complaints from voters came from the Oshkosh and Appleton areas, but voters from all over the state said they had not received the absentee ballots they requested.

Dianne Ostrowski of Waukesha, about 20 miles west of Milwaukee, said she had filed an online request for an absentee ballot but never received one.

“I’m talking via Facebook with my family in Madison. Same thing. They never got their ballot either,” said Ms. Ostrowski, who is retired from the financial services industry. Madison, the capital, is more than an hour west of Waukesha.

Tamera Goodwin and her husband, who live in Madison, also said they hadn’t received ballots. “I was looking all over the place, I was looking on the news, Facebook, my state assemblyman’s page, talking to neighbors at a distance, but everyone was confused,” Ms. Goodwin said. “None of us has gotten our ballots and none of us had clarity of where to go.”

Lacking other options, Ms. Goodwin and her husband went to vote in person on Tuesday.

In Racine, about 40 minutes south of Milwaukee, Dawn and Jeff Loken, also retired, complained that they did not receive their ballots. The two Democrats finally trudged to the polls Tuesday night, not to be deterred by what Mr. Loken, who describes himself as a “die-hard Democrat” viewed as an intentional effort by Republicans to suppress his vote. (State Republican lawmakers rebuffed the Democratic governor’s request to postpone the election.)

Some absentee voters who received their ballots and mailed them back in time are running into a separate issue: postmarking.

After much legal wrangling over this year’s absentee ballot deadlines, the Supreme Court’s decision held that ballots must be postmarked by Election Day to count. But in at least one city, Madison, a number of ballots received by the clerk were never even postmarked to begin with.

“We are still receiving mail now from the post office, and about half of it is postmarked,” said Maribeth Witzel-Behl, the city clerk. “It’s probably by now a couple thousand that we’ve received from the post office with no postmark.”

She said her office is dating the ballots with its own stamp as soon as they arrive, and is working with the city attorney to determine what to do with them.

Even when postmarks are applied, they can prove problematic, particularly for some rural voters. Michelle Schwenneker, who lives in rural Jackson County, said that the mail truck in her town comes once a day, at 7:30 a.m., so if she put her ballot in the mailbox on Election Day it wouldn’t be postmarked in time.

“For me, basically, mailing your ballot and having it postmarked are basically two different things,” said Ms. Schwenneker.

With ballots still trickling in and results yet to be released, there has been no major legal challenge to Tuesday’s election. But activist groups and election lawyers in Wisconsin are still reviewing their options and monitoring reports of missing ballots.

Even in states that already vote entirely by mail, lost ballots can plague a system. In Colorado, Secretary of State Jena Griswold excoriated the Postal Service last November after 828 ballots arrived in Denver-area mailboxes on the afternoon of a tight mayoral race in suburban Aurora — too late for many people to vote.

But perhaps nothing presented as great a challenge for Wisconsin as the vast expansion of the absentee system in such a short period of time. More than 1.2 million ballots were requested this year; only about 250,000 were issued in Wisconsin’s 2016 spring election.

Kim Wyman, the secretary of state in Washington, a mail-voting state, said it is important for elections officials to work with local postal systems to make sure they can handle the sudden increase in volume.

“These states are going from 0 to 100,” she said.

Isabella Grullón Paz contributed reporting.