REVEALED: FBI analysts thought agency's handling of case against Michael Flynn was a 'nightmare' and that some agents 'wanted a Clinton presidency'

 FBI analysts who had knowledge into the investigation of former national security adviser Michael Flynn were concerned about the agency's conduct, with some speculating that certain agents wanted Hillary Clinton to be president.

According to court filings from Flynn's lawyers, one FBI employee said the case against the former general was a 'nightmare.'

The concerns were expressed by FBI employees in the early days of the federal investigation into Flynn's ties with Russia sometime in August 2016.

According to Fox News, one FBI analyst speculated that the investigation showed that some agents 'wanted a Clinton presidency' and not a 'wild card like Trump.'

The court filings also contained text messages in which FBI analysts questioned the agency's use of national security letters to obtain Flynn's finances.

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Lawyers for Michael Flynn (above), President Trump's former national security adviser, filed papers in court containing text messages claiming to show that FBI analysts were concerned about the bureau's conduct in the investigation into his alleged ties with Russia

NSL is an administrative subpoena issued by the federal government that does not require approval from a judge.

The use of NSLs was expanded after the passage of the PATRIOT Act in the wake of the September 11, 2001, terrorist attacks.

On December 5, 2016, an FBI analyst monitoring the probe into Flynn observed that using an NSL was not a 'logical investigative step.'

FBI employees also discussed a January 5, 2017, meeting that included then-President Barack Obama, then-FBI Director James Comey, and several members of the administration.

One employee observed that 'people here are scrambling for info to support certain things and it's a mad house.'

When Trump suggested in January 2017 that a briefing on 'Russian hacking' was delayed in order to build a case, one employee said: 'Trump was right.'

On January 10, another FBI employee said that analysts 'all went and purchased professional liability insurance' over concerns that they were legally exposed due to the agency's conduct in the investigation.

'The whole thing is pretty ugly…we shall see how things pan out,' one FBI employee wrote.

The revelations came weeks after a federal appeals court in Washington declined to order the dismissal of the Flynn prosecution, permitting a judge to scrutinize the Justice Department's request to dismiss its case against Trump's former national security adviser.

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FBI analysts reportedly speculated that the Flynn probe was being waged by agents who preferred Hillary Clinton become president, according to a report. Then-FBI Director James Comey is pictured in February in Boston

The decision keeps the case at least temporarily alive and rebuffs efforts by both Flynn's lawyers and the Justice Department to force the prosecution to be dropped without further inquiry from the judge, who has for months declined to dismiss it. 

The ruling is the latest development in a criminal case that has taken unusual twists and turns over the last year and prompted a separation of powers tussle involving a veteran federal judge and the Trump administration.

The Flynn conflict arose in May when the Justice Department moved to dismiss the prosecution despite Flynn's own guilty plea to lying to the FBI about his contacts with the Russian ambassador during the presidential transition period.

But US District Judge Emmet Sullivan, who had upbraided Flynn for his behavior at a 2018 court appearance, signaled his skepticism at the government's unusual motion. 

He refused to dismiss the case and instead scheduled a hearing and appointed a retired federal judge to argue against the Justice Department's position. 

That former judge, John Gleeson, challenged the motives behind the department's dismissal request and called it a 'gross abuse' of prosecutorial power.

Flynn's lawyers sought to bypass Sullivan and obtain an appeals court order that would have required the case's immediate dismissal. 

They argued that Sullivan had overstepped his bounds by scrutinizing a dismissal request that both sides, the defense and the Justice Department, were in agreement about and that the case was effectively moot once prosecutors decided to abandon it.

At issue before the court was whether Sullivan could be forced to grant the Justice Department's dismissal request without even holding a hearing into the basis for the motion.

'We have no trouble answering that question in the negative,' the court wrote in an unsigned opinion for the eight judges in the majority.

The judges also rejected defense efforts to have the case reassigned to a different judge.