While Donald Trump and Hillary Clinton handily won the New York primary with substantial margins Tuesday, the fight hasn't ended for the state's independent voters.

A federal judge in New York heard a lawsuit Wednesday morning on behalf of "disenfranchised and purged voters in the state of New York," against the state's Board of Elections for obstructing New Yorkers from the ability to participate in the Democratic primary.

"The widespread and ongoing removal of eligible voters from the State of New York's voter-registration roll or assigned incorrect party affiliations in violation of the National Voter Registration Act of 1993, and the US Constitution's guarantee of equal protection," the lawsuit said.

"Tens of thousands of New Yorkers face the threat of disenfranchisement in the 2016 Presidential Preference Primary to be held on April 19, 2016 and will continue to be shut out of the democratic process unless and until Defendants reform the registrations practices."

Voting problems are leading people to question the whole system of a closed primary

New York's closed primary — meaning only registered Democrats and Republicans can vote in their respective parties — meant that more than 3 million voters were not permitted to participate Tuesday because they were registered outside the two political parties.

In addition, some — including those who filed the lawsuit — argue that they did follow procedures to change party voter registration, but errors eliminated them from voter rolls. Some were ultimately able to cast provisional ballots, but these problems have raised larger questions about whether a closed primary is a fair system to begin with.

Thus, voters filed a last-ditch effort Monday night to challenge the closed primary concept. Voters, mostly Democrats, filed the lawsuit against the New York State Board of Elections to open the primaries to all voters. Because a judge agreed to hear the case on Wednesday, not in time for the primary, independent voters were told to go to the polls and ask for provisional ballots.

The deadline to switch political party affiliation was last October in New York, the earliest voter registration deadline in the country. However, the plaintiffs are arguing that changes of party affiliation were lost in the mail, changed to independent without the the plaintiffs' knowledge or consent, or caught prey to clerical errors.

One plaintiff, Leonard Joseph Campanello, a 24-year-old Democrat, even provided evidence that the signature on the "change of party affiliation" form, which ostensibly proved his party affiliation had been changed from Democrat to independent, was a pixel-by-pixel replica of the signature on his driver's license that had been "electronically transferred" onto the form.

This probably won't change the results

Clinton's victory in New York Tuesday cemented her as the party's frontrunner in the delegate count. And while these voters argue they were disenfranchised in court, it is unlikely it will make a dent in Clinton's nearly 16-point win over rival Bernie Sanders.

Even for those that were able to vote, the primary process was riddled with inefficiencies and irregularities, New Yorkers reported.

Accounts of broken ballot scanning equipment, long lines stuck behind locked polling stations, and missing names and incorrect information on voting rolls were circulated widely throughout the day. More than 125,000 Democratic voters said they were incorrectly "purged" from voting lists, according to CNN.

"It has been reported to us from voters and voting rights monitors that the voting lists in Brooklyn contain numerous errors, including the purging of entire buildings and blocks of voters from the voting lists," New York Mayor Bill de Blasio said in a statement obtained by CNN, Tuesday. "The perception that numerous voters may have been disenfranchised undermines the integrity of the entire electoral process and must be fixed."

Sanders, who has the support of many people behind this lawsuit, called the day a "disgrace."

"It is absurd that in Brooklyn, New York, where I was born, tens of thousands of people as I understand it have been purged from the voting rolls," he told the rally. "It’s a little bit crazy that in upstate New York they open the polls at noon. What happens to people who get up early in the morning and have to go to work?"