It’s the clearest signal yet that the U.S.-led military campaign in Syria is widening: American warplanes on Thursday struck at al Qaeda-affiliated jihadists who attacked two groups of Western-backed rebels—fighters that the Obama administration is counting on to battle ISIS.

In an apparently improvised effort to relieve the rebels and prevent the loss of more of their strongholds close to the Turkish border, the U.S. bombed positions of Jabhat al Nusra, Al Qaeda’s Syria branch. It was a remarkable turnaround, because previously the administration had said it was avoiding attacks on the group, which used to occasionally fight alongside the American-supported rebels.

But it’s a turnaround the White House should have seen coming. In meetings of senior Obama administration officials before the first airstrikes began in Syria on Sept. 22, which hit both ISIS and al Qaeda positions, U.S. intelligence officials warned that any additional American attacks against al Nusra could drive a wedge between the group and their erstwhile allies in the American-backed, moderate opposition.

The U.S. intelligence community’s fear, according to individuals involved in the discussions, was that hitting al Nusra could draw a giant target on the rebels’ backs—which is precisely what appears to have happened. In the initial round of airstrikes in late September, the U.S. struck targets occupied both by al Nusra and a third group, an al Qaeda unit known Khorasan that U.S. intelligence agencies believed was plotting attacks against commercial airliners. Khorasan may have been the target, but Nusra was hit, too, and the impression on the ground was that the U.S. had meant to go after al Nusra all along. (Some Syrian rebel groups maintain that the Americans invented Khorasan as a pretext for the attack.) Soon after, al Nusra turned on U.S.-backed rebels, labeling them in official statements last week as “corrupt” lackeys of the Obama administration.

The administration now finds itself in the very position it had hoped to avoid, fighting a broader war against al Nusra forces and risking further alienation of Syrian civilians.

“The goal of the airstrikes has evolved from combatting ISIS in Iraq to combating ISIS and Al Nusra in Syria, because they pose an increasing threat to the opposition,” said a former U.S. official.

It’s those rebel forces that the Obama administration wanted to train and equip to help destroy ISIS. And it’s those forces that the U.S. military is now trying to save with these latest bombing raids against al Nusra.

“If the U.S. attacks Nusra without attacking Assad, all the average Syrian sees is that the U.S. is enabling, emboldening, and strengthening the Assad regime,” said Christopher Harmer, a former Navy officer and an analyst with the Institute for the Study of War, which monitors developments in Syria. “It’s not that the Syrian people love Nusra; it’s that Nusra has been in the fight against Assad, and the U.S. has looked for every excuse to stay out of the fight against Assad.”

At the time of the initial strikes, U.S. officials stressed repeatedly that the Americans were after Khorasan, not al Nusra. It was a measure of how concerned the White House was not to be seen attacking a group that enjoys popular support because of its opposition to Assad.

But Khorsan members were sharing space with Nusra fighters, living in houses alongside them, so hitting both groups was inevitable. The attacks were interpreted on the ground by Syrians trying to overthrow Assad as an attack against al Nusra, one of his main enemies, and a sign that the U.S. had no intentions of supporting efforts to topple the regime.

Now the U.S. air campaign is widening. But American officials remained reluctant to acknowledge it. “There were no strikes conducted against the al Nusra front,” Gen. Lloyd Austin, the commander of U.S. Central Command, said during remarks at the Atlantic Council in Washington on Thursday. “We did conduct a number of strikes, and the strikes were focused on the Khorasan group.”

Austin was referring to airstrikes that officials said were meant to strike another blow at the terrorist group. “We are still assessing the outcome of the attack, but have initial indications that the strikes resulted in the intended effects by destroying or severely damaging several Khorasan Group vehicles, terrorists and buildings assessed to be meeting and staging areas, IED-making facilities and training facilities,” said Maj. Curtis Kellogg, a spokesperson for U.S. Central Command. (IED stands for improvised explosive devices. Khorasan is believed to have been working with another al Qaeda division to make bombs that can be sneaked onto commercial airplanes.)

According to CNN, an American drone strike killed Khorasan’s chief bombmaker, a French jihadist named David Drugeon. If true, that would signal that U.S. military planners are getting better and more precise intelligence about Khorasan fighters on the ground in Syria. In the first round of strikes against the group, the top leaders, including Drugeon, were believed to have escaped, and there had been no indications of any strikes against Khorasan since.

Austin called Drugeon “one of the leadership elements and one of the most dangerous elements in the organization. Anytime we can take their leadership out, it’s a good thing.”

The fight with al Nusra may have been inevitable, but it risks unraveling the Obama administration’s shaky military strategy in Syria.

“Current U.S. policy—attacking ISIS without seeking an end to the Assad regime, or attacking al Nusra on some days, but not others—is strategically incoherent,” said Harmer, the Syria analyst. “As long as the U.S. strategy does not specifically seek the destruction of the Assad regime, our tactics will be at best contradictory and at worst counterproductive. “

“If the U.S. goes after Nusra, it’s an admission that our previous Syria strategy is in tatters,” said Daveed Gartenstein-Ross, a fellow at the Foundation for Defense of Democracies and an expert on terrorist groups. “What would broadening the campaign accomplish?” he asked. The root problems of jihadism that motivates fighters in the first place remains unaddressed in the military strategy, he said.

Also coming under attack from the U.S. on Thursday was a brigade that al Qaeda helped to create, Ahrar al-Sham, a hardline Islamist militia, which has assisted al Nusra in its drive against Western-backed rebels.

When al Nusra attacked the U.S.-backed rebels last week, it seized more than seven towns controlled by the rebel groups the Syrian Revolutionaries Front and Harakat al-Hazm, forcing them to run or defect. Al Nusra is now also threatening to grab control of a key border crossing into Turkey—one used by the U.S. to supply aid to favored rebel militias.

Commanders from Hazm, which has received TOW anti-tank missiles from the U.S., appealed privately to the Obama administration this week to help them to fend off the jihadists, said senior opposition sources. But a new effort to train and equip more rebels still isn’t up and running. The Defense Department has made progress in getting some training sites ready, but vetting which rebels will actually be trained there “has not begun yet,” Pentagon spokesman Rear Adm. John Kirby told reporters on Tuesday.

The UK-based Syrian Observatory for Human Rights, a pro-opposition group that gathers information from a network of activists inside Syria, said two civilians were killed in the latest air raids. The Observatory said also at least one airstrike hit buildings occupied by Ahrar al-Sham in the town of Babsalqa in the northwestern province of Idlib. One of the main founders of Ahrar al-Sham was Abu Khaled al-Souri, an emissary of Al Qaeda’s overall leader, Ayman al-Zawahiri.

The first airstrikes in September had already “put inter-rebel relations under enormous strain,” according to Faysal Itani, a fellow at the Atlantic Council. “By striking Jabhat al-Nusra without sufficiently strengthening its moderate counterparts first and promising (publicly, no less) to use them to fight Jabhat al-Nusra and not the regime, the United States made the opposition appear just threatening enough to provoke Jabhat al-Nusra, but not so threatening as to deter the jihadist group,” he argued in a paper for the think tank.

The latest raids are likely to aggravate the internecine divisions and accelerate a realignment of insurgent forces, warn rebel commanders, complicating the Obama administration’s efforts to build up a moderate rebel force. Even rebels with militias that officially are allied with the Syrian Revolutionaries Front, one of the brigades under assault from al Nusra, are expressing anger at the renewed U.S. airstrikes. “If the U.S. continues to attack al Nusra, I and my men will swear allegiance to [Abu Mohammad] al-Golani,” the group’s leader, Abu Abdullah, a SRF commander, told the Daily Beast.

Al Nusra leader Abu Mohammad al-Golani in a video posted online this week accused moderate Syrian rebel groups of being “Western collaborators.” And there are signs that al Nusra is determined to carve out an emirate of its own to rival the caliphate of the militants of ISIS, itself a breakaway from al Qaeda.

Like many rebels across the dizzying, fragmented spectrum of rebel factions—from moderates to Islamists—Abdullah argues the rebels are being set up as a sacrifice for a U.S. policy meant to prop up Iraq and defeat ISIS. And they’re furious with what they view as a cynical U.S. decision to enter the war not against Assad, but to focus instead on ISIS and jihadists.

Islamist brigades including Suqur al-Sham, a 9,000-strong militia, are openly breaking with Western-favored rebel factions. Other commanders across the squabbling insurgent spectrum are scrambling to try to broker a deal between the warring factions but say they see little signs that al Nusra is prepared to halt its offensive in Idlib province and enter a deal.

—with additional reporting by Tim Mak