Many of Trump's biggest talking points from the campaign trail -- building a wall along the southern U.S. border, a possible ban on Muslims entering the United States, climate change denials and a chummy relationship with Russia -- were discredited or disqualified by Trump's picks during their Senate hearings.
Trump is publicly supporting these differences of opinion, tweeting this morning that "All of my Cabinet nominee [sic] are looking good and doing a great job. I want them to be themselves and express their own thoughts, not mine!"
Sen. Jeff Sessions, R-AlabamaThe first such break came from Sen. Jeff Sessions, who was an active Trump surrogate during the campaign and is now his pick for attorney general. Sessions said that while he did support "extreme vetting" of people entering the United States, he stood clearly against any ban based on a religion, which was often proposed by Trump during the campaign.
"I have no belief, and I do not support the idea that Muslims, as a religious group, should be denied admission to the United States," Sessions said.
Trump's position on such a plan has evolved over time, but in December 2015 he notably called for a "total and complete" ban on Muslims entering the U.S.
Ret. Marine Gen. John KellyThe second person to face questioning was retired Marine Gen. John Kelly, who is up for the top spot at the Department of Homeland Security, which regularly deals with immigration issues. Kelly expressed concerns about relying heavily on a wall along the U.S. border.
"A physical barrier in and of itself will not do the job," Kelly said at his Senate confirmation hearing on Tuesday.
Trump has said that his "big, beautiful" wall, which was very much a cornerstone of his campaign, would be part of a multi-pronged plan to curb illegal immigration, which Trump tied to job loss and crime.
Tillerson said that "the risk of climate change does exist," which stands in contrast to Trump, who has called the idea of climate change "a hoax" and previously said it was invented by the Chinese "to make U.S. manufacturing non-competitive."
More specifically, Tillerson said he would want the U.S. to stay involved in the Paris Agreement on climate change.
"As I indicated, having a seat at the table to address this issue at a global basis and I think it's important, better served by being at that table than leaving that table," Tillerson said.
Trump has said he would "cancel" the Paris Agreement, but after the election told The New York Times that he was reconsidering his stance against the climate accord. "I'm looking at it very closely," Trump said. "I have an open mind to it."
Ret. Marine Gen. James MattisRussia was one subject that spanned multiple hearings, and while Tillerson refused to call Russian President Vladimir Putin a war criminal upon questioning by Sen. Marco Rubio, James Mattis, Trump's pick to head the Department of Defense, took a stronger stance.
"The most important thing is that we recognize the reality of what we deal with, with Mr. Putin, and we recognize that he is trying to break the North Atlantic alliance," Mattis said at his hearing Thursday, referring to NATO.
Mattis strongly defended NATO, calling it the "most successful military alliance probably in modern world history" even though Trump has repeatedly been negative about the group.
Mattis said he saw the United States "maintaining the strongest possible relationship" with NATO. "My view is that nations with allies thrive and nations without allies don't," he argued.
While Trump has publicly threatened to withdraw the United States from NATO, Mattis said he has spoken with Trump about the issue and found him "open" to his viewpoint "even to the point of asking more questions, going deeper into the issue, about why I feel so strongly, and he understands where I stand," Mattis explained.
In recent weeks, Trump has repeatedly questioned the U.S. Intelligence Community, but Mattis said he does not share that distrust. He said he has a "very, very high degree of confidence" in them.
A third area of disagreement that became clear is on the question of the Iran nuclear deal. Trump has repeatedly said that he will dismantle the deal, and Mattis stressed the importance of standing by our commitment.
"When America gives her word, we have to live up to it and work with our allies," he said.
Trump has publicly discussed another difference in stance that he and Mattis have -- Mattis does not support waterboarding -- prior to the hearing, during an interview with The New York Times in late November.
"I said, what do you think of waterboarding?" Trump said of his conversation with Mattis. "He said -- I was surprised -- he said, 'I've never found it to be useful.' He said, 'I've always found, give me a pack of cigarettes and a couple of beers and I do better with that than I do with torture.' And I was very impressed by that answer. I was surprised, because he's known as being like the toughest guy. And when he said that, I'm not saying it changed my mind."
Rep. Mike Pompeo, R-KansasPompeo, Trump's pick to be the director of the CIA, also veered away from a position Trump took during his campaign.
When asked if he would reinstate "the CIA's use of enhanced interrogation techniques that fall outside of the Army Field Manual," Pompeo said "absolutely not."
Sessions also said that torture is illegal.
Trump said during a Republican primary debate that he wants to bring back waterboarding "and I would bring back a hell of a lot worse than waterboarding."
ABC News' Luis Martinez, Mike Levine and Meridith McGraw contributed to this report.