It started when Harry collapsed.
It never really stopped.
She tried to help; told Harry it was a trap, said Kreacher would lie. But Harry was afraid, and knew the future had long since changed.
So she begged him for time and ran to find Snape.
But her definition of "time" and Harry's greatly differed, because the group was gone when she returned.
Then Snape left and she was suddenly very alone.
"...Dobby!"
"Yes, Harry Potter's friend?"
"Could you apparate any injured students at the Ministry into the Hospital Wing?"
"Yes!" A pop.
And then she waited.