The snail’s pace of California’s vote count, combined with the state’s increasing use of provisional ballots, has brought loud complaints from supporters of Vermont Sen. Bernie Sanders about the way the Democratic presidential primary was handled.

“We’ve certainly heard from people,” said Secretary of State Alex Padilla. “We’ve received phone calls here and there, but a lot on social media.”

T hose online concerns have been anything but polite.

“Are the California Primaries Rigged?” asked a story in the Bern Report.

“Bernie Sanders Wins California Landslide, but 2/3 of his Votes Aren’t Counted,” roared the Justice Gazette.

“How Bernie Won California: the official un-count,” declared NationofChange.

“There’s definitely some confusion and misinformation out there,” Padilla said.

Many of the progressive senator’s most enthusiastic supporters were shocked when Hillary Clinton won an easy California victory, particularly because polls taken in the days before the June 7 election showed Sanders and Clinton in a virtual dead heat.

Combine that with reports that many of the young and independent voters most likely to back Sanders apparently didn’t show up at the polls and confusion over how nonpartisan voters could get a Democratic presidential ballot, and conspiracy theories took wing.

Clinton’s lead drops

The final count on election night gave Clinton a 13 percentage-point lead over Sanders, 56 percent to 43 percent. But, as the late ballots and provisionals have been counted, the margin is now about 9 percentage points.

“The provisionals are breaking advantage Bernie,” said Paul Mitchell, vice president of Political Data Inc., which tracks voter information for political campaigns. “It’s not going to change the results, but Bernie’s people will get some vindication.”

Arguing that election results that don’t match the polls are proof positive of voter fraud reads way too much into those surveys, said Mark Baldassare, CEO and lead pollster for the Public Policy Institute of California, whose final pre-election poll gave Clinton a 46 percent to 44 percent lead.

“All we know is what people tell us when we’re in the field,” which doesn’t always indicate there’s a late surge coming for one candidate or another, he said.

California’s unusual primary system also drew plenty of complaints. The state’s “top two” primary system typically allows every voter — Democrats, Republicans and those with no party preference — to vote for anyone on the ballot, regardless of party.

But the rules are different in a presidential primary, where the Supreme Court has held that political parties, not the individual states, decide who votes.

While California Democrats allowed independent voters in their primary, those registered with no party preference had to specifically request a Democratic ballot. And that didn’t always happen.

There were two groups of voters who ran into problems, said Mitchell, whose firm closely tracks the vote count.

About 500,000 Californians signed up to vote right at the May 23 registration deadline, he said. Since it takes time for the counties to process the registrations and get any requested ballots in the mail, some people showed up at the polls complaining they didn’t get a ballot when county records showed they had been sent one.

“Then there were (vote-by-mail) independents who didn’t request a Democratic ballot or were put off by the need to fill out a separate card to get one,” Mitchell said. “A lot of those late registrants and independent voters were Bernie supporters.”

In California, disputes at the polling place often can be resolved with provisional ballots, which allow voters who find they aren’t listed as registered or who show up at the wrong polling place or who face some other concern to cast a ballot and have any problems resolved after election day.

“Californians should feel good about provisional ballots,” said Padilla, the secretary of state. “It’s an example of California going the extra mile to allow people to cast ballots, even if there’s a hiccup on election day.”

‘Safety net for voters’

Not everyone agrees. Since provisional ballots are separated from the rest of the votes on election day and processed separately, there have always been suggestions that the provisionals are little more than a way to placate voters at the polling places and don’t always get tallied.

“That’s kind of a common theme,” said Neal Kelley, Orange County’s registrar of voters and president of the California Association of Clerks and Election Officials. “But provisional ballots were designed as a safety net for voters, and on average about 85 percent of them are found to be valid and then counted.”

The confusion surrounding independents and the Democratic ballot resulted in a jump in the number of provisional ballots cast and counted in the state. In Orange County, for example, there were about 59,000 cast this year, compared with 40,000 in 2008 and far fewer in the years between, Kelley said.

Across California, the 2.5 million ballots left uncounted after election day included more than 700,000 provisionals, which makes California’s increasingly lengthy ballot count take even longer.

“It takes about 2½ minutes to process one provisional ballot,” Kelley said. “We can go through 15,000 to 20,000 mail ballots in a day, compared to 1,500 provisionals.”

Add the provisionals to the 1.8 million vote-by-mail ballots that had to be counted after election day because they were either turned in at the polls or arrived by the new “Postmark Plus Three” deadline and there are plenty of reasons the vote count doesn’t move swiftly.

More than two weeks after the election, state reports show that there are still 605,000 uncounted ballots in the state, and there’s little the state can do to hurry the count along.

But the delayed count can have consequences, even if the final result doesn’t change, said Ben Tulchin, lead pollster for the Sanders campaign.

While Tulchin says there’s no question Clinton won the California primary, he believes the slow ballot count still hurt Sanders.

“The election night results showed Clinton winning by 12 to 15 percentage points,” he said. “Those numbers became the national narrative,” even though the final margin may be half that.

Ensuring accurate count

Tulchin, who works from San Francisco, is no stranger to vote counting in California, but months of tracking primaries for the Sanders campaign have given him a new perspective.

“When you see how (vote counting) is done in 49 other states, you have to ask why (California’s delays) should be normal,” he said. “It’s ridiculous.”

But Padilla, a former state senator who was elected secretary of state in 2014, sees California’s weeks-long count as a good thing, both for voters and for the state.

A speedy vote count “is going to continue to be a challenge for a big state like California,” he said. “I’ve seen it from both sides, as a candidate and as secretary of state, and I’d rather take some more time to get (the vote count) right.”

John Wildermuth is a San Francisco Chronicle staff writer. Email: jwildermuth@sfchronicle.com Twitter: @jfwildermuth