Peter Rosalsky, an assistant defender with the Defender Association of Philadelphia, said judges in "nearly every single courtroom in every single county" are confronting the issue.
Criminal defense attorney Steven F. Fairlie called the situation "a mess."
Some in the legal community are hoping the quagmire will lead to a reevaluation of the practice.
"We can't correct one injustice with another injustice," said Greenleaf, who opposes mandatory minimums. "That's what the Alleyne case is trying to get at. If you're going to sentence someone, you've got to prove it."
U.S. v. Alleyne is the federal case that is the cause of the confusion.
Decided by a split majority last year, the opinion states that any fact that triggers a mandatory minimum sentence - such as the weight of drugs possessed - must be considered by a jury and proved beyond a reasonable doubt. Failure to do so, the ruling says, violates a defendant's Sixth Amendment right to a fair trial.
But in Pennsylvania, state law says a judge rules on some of those facts, including the weight of drugs or how a gun is used during a violent crime.
And the judge uses a lower standard of proof than a jury, even though those facts affect the minimum length of a defendant's sentence.
That is counter to the Alleyne decision, and defense attorneys across the state have jumped on it.
In Bucks County, for example, attorney Craig Penglase argued that a judge should not decide the weight of the drugs allegedly dealt by his client, Ingrid Rodriguez.
The District Attorney's Office argued that the solution would be simply for the jury to decide that aspect of the case as well.
But in an opinion signed by four other County Court judges last month, Judge Wallace H. Bateman agreed with Penglase and said attempts to change the way the case was adjudicated would violate current state law.
The District Attorney's Office has said it plans to appeal that decision, according to Penglase. Christopher Rees, a deputy district attorney handling the case, could not be reached.
Because similar cases have arisen in other counties, many in the legal community are hoping the state Supreme Court or the Legislature weigh in with a definitive ruling.
It's unclear how or whether those rulings would apply to cases decided during the upheaval or before the Alleyne decision was issued.
Greenleaf, however, said he would welcome an opportunity for lawmakers to reconsider mandatory minimums in general.
A former prosecutor in Montgomery County, Greenleaf said he has grown to oppose mandatory minimums "for one reason: They're not effective."
There's been no proof that mandatory minimums reduce crime, he said, referring to a 2009 study from the Pennsylvania Commission on Sentencing.
It concluded that "neither length of sentence nor the imposition of a mandatory minimum sentence alone was related to recidivism."
The main effect, Greenleaf added, has been to "fill up our prisons," which costs taxpayers tens of millions of dollars per year.
Mary Price, an attorney with the advocacy group Families Against Mandatory Minimums, said momentum is growing across the country to reduce the role of mandatory minimums.
U.S. Attorney General Eric Holder, she noted, said last year that the Justice Department would forgo seeking such sentences against certain low-level drug offenders.
Bills have also been proposed in Congress to cut mandatory minimums for other federal crimes, she said, calling the developments "quite heartening."
Greenleaf said he has perceived some momentum in the legislature to reevaluate mandatory minimums, but that he didn't believe major changes were imminent.
And first, he hopes the state Supreme Court rules on the cases affected by the Alleyne ruling, since otherwise the Legislature could be passing laws "blind."
After that, he said, lawmakers can decide whether to take up the issue.
"This has to go through this process," he said. "It's an important case for the Supreme Court to consider."