The Pentagon held a video-teleconference with Russian defense officials Saturday, two days after Russia bombed Pentagon and CIA-backed rebels not once, but twice near Syria's border with Iraq and Jordan.

The bombings killed an unspecified number of fighters.

The Pentagon said the U.S.-backed rebels were fighting the Islamic State terror group, which Russia also has bombed in the past.

The second wave of strikes unfolded after the U.S. military called Russia on an emergency hotline established following Russia's deployment of dozens of fighter jets and attack helicopters to Syria in late 2015.

On Friday, Defense Secretary Ash Carter called the Russian attacks "problematic."

“[Defense] Department officials expressed strong concerns about the attack on the coalition-supported counter-ISIL forces at the At-Tanf garrison, which included forces that are participants in the cessation of hostilities in Syria, and emphasized that those concerns would be addressed through ongoing diplomatic discussions on the cessation of hostilities,” Pentagon Press Secretary Peter Cook said in a statement.

“Officials requested Russian responses to address those concerns. The two sides reiterated the need to adhere to measures to enhance operational safety and avoid accidents and misunderstandings in the air space over Syria,” Cook said.

Russian Defense Minister Sergei Shoigu met with some of his country's pilots during a visit to Russia's airbase in Latakia, Syria along the Mediterranean coast, the Defense Ministry said Saturday. It was the same base where Russian Su-34 strike fighters launched Thursday to bomb the US-backed rebels.

The Russian defense ministry said Shoigu discussed current operations with the Russian commander in Syria, Col. Gen. Alexander Dvornikov, and inspected the S-400 air defense missile systems protecting the base, The Associated Press reported.

The USS Harry Truman, an American aircraft carrier, is steaming in the eastern Mediterranean and launching jets to bomb ISIS positions in Syria and Iraq.

These American jets have the potential to fly within range of Russian surface-to-air-missiles positioned at the Russian airbase in Syria along the coast. The Russian S-400 air defense system has a range of 250 miles.

Fox News’ Lucas Tomlinson and The Associated Press contributed to this report.