Steve Bannon, who until recently was Trump's chief strategist, accused the bishops of having an ulterior motive in advocating for families affected by the decision to revoke DACA.
Trump responded that it was "disgraceful" for the pope to question his faith.
But he said in general, removing children from families "isn't something that bears fruit for either the youngsters or their families".
"If he is a good pro-life believer he must understand that family is the cradle of life and one must defend its unity", Francis said during an in-flight press conference on his plane, according to an Associated Press report.
"As Jesus "shook" the doctors of the law to break them free of their rigidity", the Pope said, the Holy Spirit "shakes" the Church so that its members not settle into a lazy comfort, but are constantly challenged by Christ and constantly reaching out. "The pope should tell President Maduro directly to listen to the people".
"All of us have a responsibility, all of us, small or large, a moral responsibility". "I think what I see there is a fight for political interests".
The final Mass, celebrated at the docks and full of up-tempo music and worship, reiterated numerous themes Pope Francis raised throughout his trip to Colombia: peace, reconciliation and social inclusion, to name but three.
"Those who deny [climate change] should go to scientists and ask them", Pope Francis said. "Drugs, other addictions, suicides - youth suicides are very high - and this happens when they are torn from their roots". It was on a plane during the 2016 election campaign that the pope said that Trump's plan of building a wall on the Mexican border "is not Christian". "I don't know if three years is right or not, but if we don't turn back, we'll go down, that's true". We have to take it seriously.
"It's not something to play with", the pope said. Before the opening prayer, Pope Francis apologised for the wait and thanked the estimated 1.3 million people for their patience.
Pope Francis has sharply criticized climate change skeptics, saying history will judge those who failed to take the necessary decisions to curb heat-trapping emissions blamed for the warming of the Earth.
In their article, the authors cite an earlier report which asserted that if carbon dioxide emissions continue to rise beyond 2020, or even remain level, "the temperature goals set in Paris become nearly unattainable" and the UN Sustainable Development Goals agreed upon in 2015 would also "be at grave risk".
In the city of Cartagena, at his last liturgy since during his visit, he called for the "culture of death and violence" to be changed with "culture of life" to strengthen peace after signing the agreements between the last rebels and the government to end the civil war.
Politicians and diplomats can do all the right things to negotiate peace deals, he said, but if the nation's people aren't on board, peace will not be lasting.
The pontiff assured he is fine and well, the medics made all needed in such case: Pope received ice treatment and a bandage over his minor eyebrow cut.
What they were doing, he said, was saying, "This is my treasure". This is my future.