Donovan did not confirm that errant fueling was responsible, saying the Secret Service "did not have a read on what the specific issue is at this point."
The president's motorcade typically includes multiple limousines, and Obama was driven in a different vehicle.
"That's why we bring different multiple vehicles," Donovan said.
Earlier Wednesday, Obama reportedly apologized to Israeli Prime Minister Benjamin Netanyahu about the size of his entourage.
"It's embarrassing, our entourage. My wife, Michelle, teases me mercilessly," Obama said, according to the Guardian.