Special Counsel Robert Mueller and his team are facing new complications in the final stretch of their investigation into Russian meddling and potential collusion with Trump campaign associates during the 2016 presidential election, as targets allegedly breach agreements and balk at plea deals.

On Monday, the Mueller team claimed that former Trump campaign chairman Paul Manafort violated his plea deal by lying to the FBI and Mueller’s office on a “variety of subject matters,” amid reports the cooperation agreement was not panning out how prosecutors had hoped. Conservative author Jerome Corsi also plans to reject a potential deal with Mueller involving a perjury plea. Meanwhile, former Trump campaign foreign policy adviser George Papadopoulos reported to prison to begin a 14-day sentence -- but has been extremely critical of the probe on Twitter and is likely to be a thorn in the side of investigators for months to come.

The complications only served to stoke President Trump’s persistent allegations that the investigation is being unfairly run. The president tweeted early Tuesday that the special counsel’s office is treating people “viciously” and “ruining lives for them refusing to lie,” an apparent reference to Corsi's reported claims about why he won't strike a deal.

“Wait until it comes out how horribly & viciously they are treating people, ruining lives for them refusing to lie. Mueller is a conflicted prosecutor gone rogue,” Trump tweeted Tuesday morning. “The Fake News Media builds Bob Mueller up as a Saint, when in actuality he is the exact opposite. He is doing TREMENDOUS damage to our Criminal Justice System, where he is only looking at one side and not the other.”

Trump added: “Heroes will come of this, and it won’t be Mueller and his terrible Gang of Angry Democrats.”

The president, who has repeatedly referred to the probe as a “Witch Hunt” and blasted the team of investigators as “Angry Dems” based on their political affiliation and past donation history to largely Democratic candidates and causes, submitted his written answers to Mueller’s questions in the probe last week, marking a major milestone in the investigation. His attorneys said that despite their serious issues with the probe, the president has provided “unprecedented cooperation.”

Mueller is widely expected to be nearing the final stages of the investigation in the wake of the November midterms.

But in a late twist, a court filing Monday night said Manafort, who was convicted on multiple counts of financial fraud over the summer in connection with work he completed in Ukraine as a political consultant, breached the plea deal agreed upon earlier this year.

“After signing the plea agreement, Manafort committed federal crimes by lying to the Federal Bureau of Investigation and the Special Counsel’s Office on a variety of subject matters, which constitute breaches of the agreement,” Mueller’s office said.

One source told ABC News on Monday that special counsel prosecutors were “not getting what they want” from Manafort.

In a joint-status report, Manafort contested the special counsel’s claims, noting that he met with the government “on numerous occasions and answered the government’s questions.”

“Manafort has provided information to the government in an effort to live up to his cooperation obligations,” his lawyers wrote. “He believes he has provided truthful information and does not agree with the government’s characterization or that he has breached the agreement.”

Manafort’s sentencing in the Eastern District of Virginia is, at this point, slated for early February.

Also Monday night, Corsi, who revealed earlier this month that he had received a subpoena in the investigation, told The Associated Press that he plans to reject any deal offered to him to plead guilty to perjury.

He claimed to reporters they wanted him to admit to something he didn't do, and effectively lie in doing so.

Corsi is closely connected with GOP political operative Roger Stone, who also expects to be a target in Mueller’s probe. Stone has said he believes Mueller is investigating whether he had advanced knowledge of WikiLeaks releasing hacked emails of Democrats during the campaign.

In a statement to Fox News on Monday, Stone denied advance knowledge of email hacking.

“I continue to see that my friend Dr. Jerry Corsi is being harassed by the Special Counsel, not for lying, but for refusing to lie,” Stone said. “It is inconceivable that in America someone would be prosecuted for refusing to swear to a false narrative pushed on him by the Mueller investigators.”

Stone added: “If Jerry ever deduced that Mr. Podesta’s emails had been purloined and would be published by WikiLeaks, he did not share that conclusion with me.”

CONSERVATIVE WRITER JEROME CORSI REJECTS POTENTIAL MUELLER PLEA DEAL

Corsi said earlier this month his ongoing negotiations with the special counsel have “just blown up,” even though he said he “did everything” he could to cooperate and thought he was “doing a pretty good job of it.”

“This has been one of the most frightening experiences of my life,” Corsi said.

Meanwhile, Papadopoulos, who pleaded guilty to making false statements to the FBI last year, was sentenced to 14 days in prison, where he reported Monday. Papadopoulos has been outspoken on Twitter and in media interviews regarding the nature of the investigation and his experience with the special counsel’s office.

“The truth will all be out. Not even a prison sentence can stop that momentum,” Papadopoulos tweeted Sunday. “Looking forward to testifying publicly shortly after. The wool isn’t going to be pulled over America’s eyes forever. Much love.”

One of the first high-profile targets, though, has yet to be sentenced. Next month, after a year of delays, the special counsel has scheduled a sentencing date for former National Security Adviser Michael Flynn, who also pleaded guilty to making false statements to the FBI with regard to conversations with then-Russian Ambassador Sergey Kislyak during the transition as part of a plea deal

Mueller’s team has repeatedly delayed Flynn’s sentencing, raising questions and fueling GOP concerns over the status of the investigation, but the retired three-star Army general is expected to finally be sentenced on Dec. 18.

In addition to problems with the Trump campaign-connected targets, Mueller’s team has faced challenges pursuing the case against a slew of Russian companies and citizens. In February, a federal grand jury indicted 13 Russians and three Russian companies for allegedly acting as a troll farm interfering in the 2016 presidential election and waging “information warfare” against the U.S.

But Washington attorneys then surfaced to fight back on the Russians' behalf, even seeking sensitive evidence from Mueller's team.

Fox News’ Jake Gibson, Alex Pappas, Matt Richardson, and The Associated Press contributed to this report.