Special counsel Robert Mueller has been pursuing several Russia collusion leads even as a number of media outlets say his final report is due soon, according to court filings and sources.

Former acting Attorney General Matthew G. Whitaker said in January that he had been read-in on the nearly two-year probe and concluded it was “close to being completed.”

But there are signs that Russia issues remain:

• Court filings in the prosecution of former Trump campaign manager Paul Manafort show that Mr. Mueller is still investigating a fall 2016 meeting at a Manhattan cigar bar where the lifting of U.S. sanctions on Russia was discussed.

• Mr. Mueller still has questions about the Ukraine amendment to the 2016 Republican Party platform.

• The indictment of Trump political adviser Roger Stone for allegedly lying to Congress sets up the possibility of a plea bargain. Mr. Stone has denied wrongdoing and has said he will never betray President Trump. But he has added that he is willing to cooperate.

On Manafort, a closed hearing for which a sanitized transcript was released showed Mueller senior prosecutor Andrew Weissmann is still probing the August 2016 meeting between Manafort, his ex-business partner Rick Gates and Ukraine-born Constantine Kilimnik. Mr. Kilimnik, a former low-ranking translator for Russian military intelligence, was a Manafort translator and office manager in Ukraine for a decade.

Gates has turned state’s evidence. The transcript indicates he has made a new allegation against Manafort dealing with sanctions relief that could in some way be tied to a conspiracy.

“This goes, I think, very much to the heart of what the special counsel’s office is investigating,” Mr. Weissmann told U.S. District Judge Amy Berman Jackson.

Judge Jackson agreed with Mr. Weissmann’s allegation that Manafort lied about the meeting during his government cooperation phase.

Defense attorney Kevin Downing called Mr. Weissmann’s theory “nonsense because no matter who gets elected, that the sanctions were going to continue against Russia. I think you need to consider this rank speculation.”

A Manafort supporter told The Washington Times, “There is no evidence of collusion.”

Manafort was sentenced on March 8 to just shy of four years in prison for tax and bank by fraud by U.S. District Judge T.S. Ellis III in Virginia.

Judge Jackson tacked on an additional 43 months at a March 13 hearing in Washington, D.C., for lobbying violations and witness tampering.

Judge Jackson, an Obama appointee, scolded Mr. Downing for saying there is no evidence of Manafort-Russia collusion. She said the Mueller investigation continues.

In a court filing, Mr. Downing said: “The Special Counsel’s strategy in bringing charges against Mr. Manafort had nothing to do with the Special Counsel’s core mandate — Russian collusion — but was instead designed to ‘tighten the screws’ in an effort to compel Mr. Manafort to cooperate and provide incriminating information about others.”

On the Ukraine question, Mr. Mueller still hasn’t closed his inquiry even though Republicans believe they have debunked the tale.

The charge is that while the Republican platform was being written at the Cleveland convention, Trump operatives took out language that would have encouraged lethal aid to Ukrainian forces fighting Russia-backed separatists.

In reality, a single delegate offered the lethal aid amendment for inclusion. It was never in the platform. Trump people, not wanting to commit a new administration to arming Ukraine, reached a compromise. The new language pledged support to the Ukrainian military.

The Republican majority of the House Permanent Select Committee on Intelligence reviewed the various platform drafts and concluded the final product was stronger, not weaker, on Ukraine.

The issue is still alive among Democrats in Congress. House Judiciary Committee Chairman Rep. Jerrold Nadler of New York sent 81 document-demand letters to various Trump-linked people and entities. Some letters asked for any information on the Ukraine platform language.

On Roger Stone, his friends told The Times that it is obvious the Mueller team wants to flip him to incriminate Trump campaign personnel. Mr. Stone repeatedly has said he has no evidence against the president.

The deployment of nearly 30 FBI agents, some equipped with rifles and bulletproof vests, in a pre-dawn raid to arrest him at his Florida home is evidence of government intimidation, Mr. Stone’s friends say.

The indictment said he lied to the House Intelligence Committee. He denied owning any emails or text messages pertaining to his efforts to find out when WikiLeaks would release the next batch of Russia-stolen Democratic Party memos. Mr. Stone, in fact, did have such documents. The indictment said he communicated with unnamed Trump campaign people.

One of those campaign people was Mr. Trump himself, according to his former attorney, Michael Cohen, who has pleaded guilty to tax and campaign finance counts. Today he is Mr. Trump’s prime accuser, touching off probes by state Democratic officer holders in New York into the Trump Organization real estate empire.

Cohen provided this Trump Tower scene to the House Oversight and Government Reform Committee: “In July 2016, days before the Democratic convention, I was in Mr. Trump’s office when his secretary announced that Roger Stone was on the phone. Mr. Trump put Mr. Stone on the speakerphone and Mr. Stone told Mr. Trump that he had just gotten off the phone with Julian Assange and that Mr. Assange told Mr. Stone that within a couple of days there would be a massive dump of emails that would damage Hillary Clinton’s campaign. Mr. Trump responded by stating to the effect, ‘wouldn’t that be great.’”

Mr. Stone text messaged The Hill newspaper denying Cohen’s story.

Mr. Stone says today that he never communicated with Mr. Assange, who in turn says he never communicated with Mr. Stone or the Trump organization.

Mr. Stone says he remains unconvinced that Russia hacked Democratic Party computers and provided emails to WikiLeaks, as U.S. intelligence says.

The Stone indictment doesn’t charge him with conspiring with Russia.

The Times asked Stephen A. Saltzburg, a George Washington University law professor and associate independent counsel in the Iran-Contra probe, if Mr. Mueller can file a final report while some issues are pending.

“It seems there will come a point where he might decide he can’t get the final answer. That happens,” Mr. Saltzburg said.

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