It was a last-minute scramble to have actor Chris Evans fill in for Stone's boyfriend Garfield, 30, during the Oscar ceremony.
Pals close to the couple reveal their absence must have been for a serious reason.
"It was disheartening to learn that Andrew canceled on the Oscars," an insider told Radar.
"If it were a fight or something between them one would have just came without the other, but this seemed to be more of something going on with one of their families."
Another source told Radar that Stone, 25, had a long standing family commitment in Arizona.
The insider said it must have been something important for them to miss a highly publicized appearance.
"With Emma, it's all family first. And Andrew is so devoted to her that he wouldn't just leave her in New York dealing with some sort of crisis on her own," the source said.
Stone's mother, Krista Stone, was diagnosed with triple negative breast cancer in 2008 — a case that is known to be highly aggressive and notoriously tough to treat.
Stone and her mother are very close and even got matching blackbird tattoos to celebrate five years cancer-free in 2013.
"Emma and Andrew don't have any other press obligations in the next two weeks, so hopefully whatever it is, they will have some time to themselves to deal with it," the source concluded.