Donald Trump was at odds with his running mate on Sunday night, telling the moderators during the second presidential debate that he disagreed with Mike Pence’s opinion on Russia’s role in Syria.

During a discussion about the humanitarian crisis in Aleppo, ABC’s Martha Raddatz reminded the GOP nominee what Pence had said about the issue during Tuesday's vice presidential debate.

“And I want to remind you what your running mate said,” Raddatz said. “He said ‘Provocations by Russia need to be met with American strength, and that if Russia continues to be involved in airstrikes along with the Syrian government forces of [President Bashar] Assad, the United States of America should be prepared to use military force to strike the military targets of the Assad regime.”

Trump immediately replied: “Okay. He and I haven’t spoken and I disagree. I disagree. I think you have to knock out ISIS.”

Trump went on to explain that his entire focus in Syria rested on eliminating ISIS by whatever means necessary – and via whichever country could best achieve that goal.

But Trump’s “I disagree” comment was striking, particularly as the fallout from Trump’s controversial 2005 hot mic remarks continues to play out. Various media reports have portrayed Pence as being anguished by Trump’s 11-year-old remarks and perhaps even contemplating removing himself from the GOP ticket – reports that the Trump campaign has strongly denied.

A campaign source told Fox News that “Trump and Pence had a lengthy and very positive phone call post debate.” Pence tweeted congratulations to Trump after the debate, as well.

Trump’s previous praise of Russia and President Vladimir Putin have also been discussed in previous primary and general election debates.

The position Pence staked out during the vice presidential debate regarding Russian involvement in Syria immediately raised questions on if Pence was at odds with the top of the ticket.

Fox News' Daniel Gallo contributed to this report.