TLDR We really have no way of knowing with publicly available information.
Before I dig into the meat of this, I want to point out on the subject of Flynn specifically it should be noted that while his name wasn't masked in that call, it was masked in others (emphasis mine):
Then-Director of National Intelligence James Clapper also made an unmasking request for Flynn on Dec. 2, 2016, which also was prior to the Kislyak conversations; then-CIA Director John Brennan made requests on Dec. 14 and Dec. 15, 2016; and then-FBI Director James Comey made a request on Dec. 15, 2016.
So the claims that Flynn was never "unmasked" are slightly misleading here. Yes, that call never had him masked in the first place, but others did. We now have a list of people involved with the unmasking though whether it is significant remains to be seen (emphasis mine):
MYRE: So just after the 2016 election, Michael Flynn is named national security adviser. And he calls the Russian ambassador in Washington. The U.S. is listening in to this call because they're quite interested in the Russian ambassador. They're still trying to determine the role of Russian interference in the election. And they hear Flynn. When they print up the document, they redact his name. But officials in the Obama administration request the name of this person, not knowing who it is but then finding out that it's Flynn. The process works. It's approved. The material is sent over to these administration officials.
Now, we don't know exactly who read it and who didn't, but Joe Biden was one of those involved. We do know that. Flynn ultimately lasted less than a month in office. Trump said he lied about his contacts with Russian officials. And and he ultimately pleaded guilty to lying, although his case is still playing out, as we've heard in recent weeks.
CHANG: So is there any sign that something improper was done here?
MYRE: No. We want to be very clear about that. The two senators who released this, Republicans Ron Johnson of Wisconsin and Charles Grassley of Iowa - they said that these records they released are one step toward an important effort to get to the bottom of what the Obama administration did. But they're not alleging any wrongdoing at this point. Trump, meanwhile, has been talking about something he calls Obamagate and that there were crimes committed. But he's not making any specific charge. And a lot of critics are saying he's just trying to create an election year controversy but really doesn't have any substance to back it up.
So, back to the main question here, as this ever happened before? We don't really know. Most of the processes about what happens in FISA Courts is classified.
The names of the judges on the Foreign Intelligence Surveillance Court are public. But good luck trying to read the thousands of wiretap orders the court has approved since it was created in 1978. They are all secret.
The same article goes on to say that "victims of FISA wiretaps" may not even "know they were bugged:"
Ordinary wiretaps are sometimes challenged by defendants once they are charged, but victims of FISA wiretaps almost never even find out they were bugged. In 2008, a group of activists and journalists challenged a law that expanded this court's authority. They argued that their communications put them at risk of being caught up in government wiretaps. But earlier this year, the Supreme Court said these people could not show they had in fact been monitored, so it threw their suit out.
A moment of irony here: you might be secretly wiretapped but can't do anything about it because you can't prove you were secretly wiretapped. That's kind of seems like a Catch 22 if you ask me.
This whole situation is part of what happened in the Snowden controversy. He revealed the government had the authority to perform what some have called "legal warrantless searches:"
The National Security Agency has a secret backdoor into its vast databases under a legal authority enabling it to search for US citizens' email and phone calls without a warrant, according to a top-secret document passed to the Guardian by Edward Snowden.
Even though this has raised questions about whether abuse could occur an investigation into the matter in 2014 found "no indication of abuse":
Depending on the scope of collection, however, the applicable rules may allow a
substantial amount of private information about U.S. persons to be acquired by the
government, examined by its personnel, and used in ways that may have a negative impact
on those persons. Although it is not known how many communications involving U.S.
persons or people in the United States are acquired under Section 702, the limited figures
available may provide some indication of the extent to which the government presently
could be using such communications. Some of these figures illustrate that the Section 702
program remains primarily focused on monitoring non-U.S. persons located outside the
United States. By the same token, the overall scope of collection under the program and the quantity of intelligence reporting derived from this collection involving U.S. persons
suggest that the government may be gathering and utilizing a significant amount of
information about U.S. persons under Section 702.
If so, this would raise legitimate concern about whether a collection program that is
premised on targeting foreigners located outside the United States without individual
judicial orders now acquires substantial information about U.S. persons without the
safeguards of individualized court review. Emphasizing again that we have seen no
indication of abuse, nor any sign that the government has taken lightly its obligations to
establish and adhere to a detailed set of rules governing the program, the collection and
examination of U.S. persons’ communications represents a privacy intrusion even in the
absence of misuse for improper ends. The Board’s desire to provide more clarity and
transparency regarding the government’s activities under Section 702, particularly insofar
as they involve the acquisition and handling of U.S. persons’ communications, underlies a
number of our recommendations.
Of course, it is worth noting that this is a governmental organization investigating the government, so it's unclear whether you can really trust them when they say this. But to be fair I guess I'll give them the benefit of the doubt here for now.
Worth noting that while what happens in FISA courts is usually classified, there have been efforts in recent years to declassify actions taken by the intelligence community, starting with the Obama administration in 2013:
In June 2013, President Obama directed the Intelligence Community (IC) to declassify and make public as much information as possible about certain sensitive U.S. government surveillance programs while protecting sensitive classified intelligence and national security information.
Since then, the Director of National Intelligence has declassified and authorized the public release of thousands of pages of documents relating to the use of critical national security authorities, including the Foreign Intelligence Surveillance Act. In addition to declassifying and publicly releasing these documents, the Intelligence Community has published several reports regarding these authorities, including the Statistical Transparency Report Regarding use of National Security Authorities, presenting metrics related to the use of certain authorities for calendar years 2013 and 2014 .
So while information on the FISA court's actions is currently little to none, that may change in the future, given that the Trump administration seems to have continued in Obama's footsteps in that regard by releasing a "Statistical Transparency Report" for the calendar years of 2017 and 2018.
In the mean time, though, we really have no way of knowing without having access to classified documents.