Facebook is facing new questions over its handling of the Cambridge Analytica debacle even after a record settlement with the FTC ended a year-long investigation by regulators into the matter.

Facebook has maintained that it first became aware of Cambridge Analytica's illegal harvesting of user data in December of 2015, when The Guardian first reported it.

But internal emails from Facebook employees, first described in a lawsuit from the attorney general for Washington, D.C. in March, show that Cambridge Analytica had been flagged within the company as early as September 2015 over suspicions that it had been “scraping” Facebook data in violation of the platform’s policies.

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Those warnings were further detailed last week, in a filing from the Securities and Exchange Commission (SEC) as part of that agency’s $100 million settlement with Facebook over charges that it misled investors about the material risk of the scandal.

Months before the Guardian first revealed that Cambridge Analytica had obtained data on tens of millions of Facebook users without their knowledge, Facebook employees had requested an investigation of the right-wing political consulting firm over suspicions it had misused data.

Before declaring bankruptcy last year as a result of the debacle, Cambridge Analytica had deep ties with the Republican party and in 2016 worked for the Trump campaign, assembling voter profiles based on data from a range of sources, including social media sites.

After the Guardian story ran, the employees again raised concerns about Cambridge Analytica, describing it as a “sketchy (to say the least) data modeling company that has penetrated our market deeply,” according to the SEC complaint.

The SEC’s filing has raised further questions from the UK Parliament, where MP Damian Collins, who chairs the Digital, Culture, Media and Sport Committee (DCMS), has been investigating the data scandal. Collins sent a letter to Facebook on Thursday saying that the complaint “seemingly directly contradicts” testimony that the company has offered to the committee.

“We have serious and justifiable concerns that, despite the significant and continuous red flags raised by Facebook employees about Cambridge Analytica since potentially as early as September 2015, these incidents did not reach senior management, deliberately or otherwise,” Collins wrote.

“We therefore request that you respond to our concerns as to why senior management, including [CEO] Mark Zuckerberg Mark Elliot ZuckerbergKey Democrat opposes GOP Section 230 subpoena for Facebook, Twitter, Google Many Google staff may never return to office full time Hillicon Valley: FBI, DHS warn that foreign hackers will likely spread disinformation around election results | Social media platforms put muscle into National Voter Registration Day | Trump to meet with Republican state officials on tech liability shield MORE, were not informed about these incidents until they were reported in the press,” he added. “We believe this to be particularly egregious given that we have been told that these issues should have been reported through senior management and that the buck ultimately stops with Mr. Zuckerberg himself.”

Facebook declined to comment on the letter, but the company has said that the activity deemed suspicious by employees prior to the Guardian story was different from the partnership between Cambridge Analytica and the creator of a personality quiz app that collected the user data.

David Carroll, a professor at the Parsons School of Design, whose battles with Cambridge Analytica were the focus of the recently-released Netflix documentary “The Great Hack,” said there are still plenty of open questions about Facebook’s handling of the incident.

“I share the questions about the timeline of who knew what when,” Carroll told The Hill. “Even if you believe Zuckerberg, that he learned about it in The Guardian in December 2015 — even if that's true, it means that he has a sort of catastrophical management problem that it didn't get escalated to the C-suites."

Facebook is currently fighting to keep the September 2015 emails sealed as it tries to fend off a lawsuit from Washington, D.C. Attorney General Karl Racine (D).

The emails were first detailed in a filing in the case earlier this year. And on Friday, the two sides squared off in court over whether the records should be unsealed. Racine’s office argued that the substance of the emails has already been alluded to by the SEC and should be included in the court record and released to the public.

“This document has now been referred to, has been directly quoted, by the Securities and Exchange Commission,” Jimmy Rock, an attorney in Racine’s office, said in court Friday. “So here there cannot be legitimate prejudice at this point to Facebook with the document of direct quotations and the substance of it being part of the public record."

Facebook argued the emails should remain under seal because they contain sensitive information about the company's practices and are "irrelevant and unnecessary to these proceedings."

Those emails aren’t the only part of the timeline drawing extra scrutiny from Facebook’s critics. In June of 2016, Facebook and Cambridge Analytica reached a settlement that required the consulting group to delete all of the data it had obtained through researcher Aleksandr Kogan’s app.

In his letter on Thursday, Collins noted red flags that arose in the months after that should have tipped off Facebook’s management that the group was still abusing user data to create voter profiles for clients like President Trump Donald John TrumpSteele Dossier sub-source was subject of FBI counterintelligence probe Pelosi slams Trump executive order on pre-existing conditions: It 'isn't worth the paper it's signed on' Trump 'no longer angry' at Romney because of Supreme Court stance MORE's 2016 campaign.

A Washington Post article that ran days before the presidential election, for example, noted that Cambridge Analytica was using “psychological tests” combined with data from “social-media sites.”

And as the SEC wrote in its complaint, “As an additional indication to Facebook that Cambridge might have been misusing Facebook user data, some employees on Facebook’s political advertising team knew from August 2016 through November 2016 that Cambridge named Facebook and Instagram advertising audiences by personality trait for certain clients that included advocacy groups, a commercial enterprise, and a political action committee.”

The renewed scrutiny comes as the FTC is under fire for its own settlement with Facebook despite imposing a headline-dominating $5 billion fine for the company. Critics, including officials at the agency, have criticized the agreement for not doing more to curtail Facebook’s business practices or putting more of a check on the decision-making powers of Mark Zuckerberg, who serves as both CEO and chairman of the board of directors.

The FTC did not interview Zuckerberg as part of its year-long investigation into the scandal, likely because Facebook would have fiercely opposed the move, escalating the possibility that it would lead to a lengthy, high-profile court battle.

“The last thing Zuckerberg’s handlers would do is subject him to deposition by an FTC attorney. Depositions are serious and more of a crucible than a congressional hearing,” Chris Hoofnagle, a law professor at University of California, Berkeley, said in an email to The Hill. “If I were Zuckerberg’s lawyer, I’d do anything to keep him away from a direct interaction with the FTC lawyers.”

With Facebook still struggling to turn the page from the Cambridge Analytica fallout, there will also be lingering questions over how regulators handled the investigation.

“People wonder why the FTC always settles,” Hoofnagle added. “It’s actually the defendants that want to settle. The FTC investigates and invariably uncovers other wrongdoing and knowledge of the action by executives.”