Get breaking news alerts and special reports. The news and stories that matter, delivered weekday mornings.

In the chaotic first days after President Donald Trump closed the United States' borders to refugees and citizens from seven Muslim-majority countries, protests, legal uncertainty and panic gripped airports and minority communities.

Now critics are scrambling to fight the order they've dubbed a "Muslim ban" while supporters seek to defend and clarify the order, even as the government itself scrambles to understand and address the implications of the order.

Related: Department of Homeland Security Seeks to Quell Confusion Over Refugee Ban

Confusion continues to overwhelm the order. After green card holders were detained over the weekend amid the uncertainty, senior White House administration officials said green card holders from the seven affected countries wouldn't be subject to the ban.

But White House Chief of Staff Reince Priebus left the door open to more questions Sunday when he said border officials may use their "discretion" to question those legal permanent residents to make sure they are not "up to no good."

Newly installed Homeland Security Secretary John Kelly appeared to settle the matter with a statement Sunday evening saying that in the absence of "significant derogatory information indicating a serious threat," allowing entry to green card holders was in "the national interest."

His agency, the Department of Homeland Security, is responsible for enforcing Trump's ban, and it sought to quell reports that it was not complying with emergency court rulings that temporarily halted parts of the order.

Adding to the uncertainty: State Department officials said Monday that the status of individuals who have dual citizenship — British and Iranian citizenship, for instance — was still unclear, after initially saying those people would be caught up in the visa bans.

Sen. Marco Rubio, R-Florida, a member of the Foreign Relations Committee, told reporters Monday night that the State Department staff had been "ordered not to talk to Congress" about the executive order.

"I don't know the reason," Rubio said. "Maybe, perhaps, they're still kind of working through how this is going to apply, and so perhaps they don't want to give us information that is wrong."

Let our news meet your inbox. The news and stories that matters, delivered weekday mornings. This site is protected by recaptcha

State Department spokesman Mark Toner said, "The Department remains in contact with Members of Congress who have reached out regarding the Executive Orders, and will continue to provide information and assistance as we are able."

Rubio was also critical of the Trump administration's roll-out of the executive order, saying he wishes it would have consulted more with both Congress and the agencies affected by the order.

The White House forcefully defended the order over the weekend and Monday, saying that just 109 — out of 325,000 who entered the United States on Friday — were detained for further questioning after landing in America in the immediate wake of the ban before being all released.

And a State Department spokesman told NBC News on Monday night that about 900 refugees who were in transit when the order was released will be granted an exemption and admitted to the United States this week. The number doesn't include nationals from Iran, Iraq, Sudan, Syria, Somalia, Yemen or Libya, the spokesman said.

White House Press Secretary Sean Spicer argued at Monday's news briefing that "being able to come to America is a privilege, not a right," and that the "temporary inconvenience" was a small price to pay for the country's national security.

"I don't think it's a big problem," Spicer said.

Federal agencies were still scrambling to implement and decipher the order Monday, in part because it appears that many weren't consulted in advance.

Spicer told reporters that "there was staff from appropriate committees and leadership offices that were involved," but NBC News confirmed that two House Republicans heading key committees that oversee immigration legislation weren't consulted: Homeland Security Chairman Michael McCaul of Texas and House Judiciary Chairman Bob Goodlatte of Virginia.

Several House leadership aides told NBC News that they also weren't consulted. In fact, aides said, they received the text of the executive order at the same time the news media did Friday night.

The White House's efforts to downplay the order was challenged by human stories of octogenarian grandparents' and young children's being detained for hours of questioning, while others were barred from boarding planes to return to homes and family in the United States.

Their stories sent thousands of people to airports and Trump's luxury hotel in Washington, D.C., in protest and prompted others to donate to the American Civil Liberties Union, which said it had raised $24 million since Saturday.

The ACLU and other advocates put forward legal challenges to the order almost immediately, winning two emergency court orders — including several delaying enforcement of parts of the order — and at least seven other lawsuits are open or were expected to be filed on Monday seeking to overturn the ruling.

Legal hearings take weeks to move forward, but there likely will be test cases as dual nationals and other people challenge the new rules.

Sen. Chris Murphy, D-Connecticut, said Sunday on Twitter he has a bill planned for "this week" to put a stop to what he called a "dangerous, hateful order," while Senate Minority Leader Chuck Schumer, D-New York, tried to force a vote on the Senate floor to overturn the order Monday.

Although Schumer's move failed, as he needed all 100 senators to agree to a vote, a few cracks in party lines have emerged as a handful of Republicans broke with Trump on Sunday to speak out against the order.

The most prominent Republicans to criticize the ban were longtime hawks John McCain of Arizona and Lindsey Graham of South Carolina, who said the order was "not properly vetted."

"Ultimately, we fear this executive order will become a self-inflicted wound in the fight against terrorism," Graham and McCain said, earning a pair of scolding tweets from the president.

...Senators should focus their energies on ISIS, illegal immigration and border security instead of always looking to start World War III. — Donald J. Trump (@realDonaldTrump) January 29, 2017

...Senators should focus their energies on ISIS, illegal immigration and border security instead of always looking to start World War III. — Donald J. Trump (@realDonaldTrump) January 29, 2017

House Democrats on Monday also introduced the Statue of Liberty Values Act, or SOLVE, to block Trump's order. However, the legislation will likely go nowhere as Democrats are in the minority.

Acting Attorney General Sally Yates, meanwhile, issued a letter instructing the Justice Department to "not present arguments in defense" of Trump's travel ban.

"At present, I am not convinced that the defense of the Executive Order is consistent with these responsibilities nor am I convinced that the Executive Order is lawful," Yates wrote.

The Justice Department's Office of Legal Counsel signed off on the policy last week — Yates in her letter notes that her role is different from that of the OLC — and Justice Department lawyers did defend the policy in court over the weekend.

Trump, for his part, has tried to change the conversation: He announced a new executive order on business regulations on Monday, as well as tweeting that he'd announce a Supreme Court pick on Tuesday night.