It was supposed to be the first of many large-scale court hearings to ­address potentially flawed drug cases linked to former state chemist Annie Dookhan.

But after 19 inmates were transported from prison and jail cells Friday to appear in Boston Municipal Court, only five were found to have cases affected by Dookhan’s alleged mishandling of drug evidence at the now-closed state Department of Public Health drug lab in ­Jamaica Plain. Of those, two were ­released, and three were assigned court dates.

As attorneys waded through the pool of unrelated cases, Suffolk District ­Attorney Daniel F. Conley laid blame for the confusion with “the leadership here at the Boston Municipal Court.”

“This list here, no one can make any sense of how it was produced in this courthouse,” he said.

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Two other cases related to Dookhan were in the spotlight in Suffolk Superior Court, resulting in the release of one man and the reinstatement of bail for another who had just been released.

As many as 1,142 people could be ­released statewide as a result of the scandal, authorities have said. Conley said on Friday that 300 to 500 of them could be released in Suffolk County, including “some pretty dangerous people.”

Conley wrote a letter to Robert A. Mulligan, the trial court’s chief justice of administration, blasting Chief Justice Charles Johnson for not giving his office enough notice to review the 19 cases called in Boston Municipal Court Friday to determine if they were connected to Dookhan. Conley said the list arrived in his office Thursday afternoon.

“If you’re puzzled by what’s going on in that courtroom, so am I, and I regret that this is an example of what happens without proper planning,” Conley said.

The cases of two men, Carlos Colon and Michael Wells, were connected to Dookhan. Colon’s bail was ­reduced to $500 and he was ­released; Wells was released on personal recognizance.

According to police reports, Colon, 22, was seen by police selling crack cocaine in April 2010 near Cathedral Grammar School in the South End, and Wells, 24, sold crack cocaine to an undercover officer in March 2010, on Washington Street in Roxbury.

Dookhan played a role in drug testing in both cases, accord­ing to authorities.

When asked if she believed her client would be tried, Marcy Levington, ­Colon’s lawyer, said prosecutors “have no drugs.’’

“I think it’s a mess; I think it will take months for us to sort through it all,’’ she said.

Three other men — Nathan Adams, Richard Brown, and Christopher Ortiz — were given court dates when their lawyers will probably ask a judge to stay execution of their sentences.

Less than a half-mile away, in Suffolk Superior Court, the man whose case is now serving as the means to prosecute Dookhan had all criminal charges against him in Suffolk County dropped by prosecutors because Dookhan has allegedly admitted faking the test results.

Jeffrey Solomon showed no emotion when Judge Carol Ball approved the request by ­Conley’s office to drop the charges.

From the bench, Ball credited Suffolk prosecutors for “acting with honor” in the Solomon case and in other prosecutions with links to Dookhan.

Unlike other defendants who have been released from custody because Dookhan handled evidence in their cases, Solomon was returned to a Depart­ment of Correction cell where he is serving a maximum four-year sentence on drug charges and intimidating a witness in an unrelated case.

Still, his attorney, Victoria Kelleher, said Solomon is planning to file a civil lawsuit because he was held in jail due to the Suffolk County charges that are now found to have been based on false information.

“There certainly has been a violation of his civil rights,’’ Kelleher said.

Kelleher said she wants a Boston police officer investigated for allegedly perjuring himself. She said the officer who ­arrested Solomon field tested the drugs and found they were counterfeit, leading to Solomon first being charged only with trying to sell counterfeit drugs.

But once Dookhan certified that the substance that was seized was cocaine, the officer allegedly testified before a grand jury that the field test sample had turned blue since Solomon’s arrest, meaning the field test was also positive for the presence of cocaine.

Cheryl Fiandaca, a police spokeswoman, defended the ­officer involved in the Solomon case saying he has an “unblemished record” and he “testified truthfully in the grand jury.”

Dookhan is free on $10,000 bail after pleading not guilty in Boston Municipal Court to two counts of obstruction of justice, one the alleged fabricating of evidence in Solomon’s case.

According to a spokeswoman for Middlesex District Attorney Gerard T. Leone Jr., prosecutors there are now checking their records to see whether there is a Dookhan connection to their case against Solomon.

Solomon pleaded guilty earlier this year to charges that grew out of a Cambridge police investigation in 2009, the same year that Leone’s office stopped using the Jamaica Plain lab.

Also Friday, officials arrested Marcus Pixley, a Suffolk drug defendant whose bail was ­reduced as part of the drug lab fallout and who then missed a court date.

A convicted rapist, Pixley ­appeared to have been among the first of the defendants freed because of the scandal to land in legal trouble again. He was arraigned and held on $2,000 cash bail.

“I’m not going to plead guilty to something that I didn’t do,” he yelled from a hallway in Suffolk Superior Court.