Left on the bench for a win over Guatemala last week, Dybala again missed out on a starting spot in New Jersey on Tuesday, introduced early in the second half in the 0-0 draw against Colombia.
But Scaloni rubbished any talk he had an issue with Dybala, who was expected to be given more of a chance in Lionel Messi's absence.
"You think I have a problem with him? He's a phenomenon," Scaloni said.
"What happened is we didn't train during the week. It's a big one."
He added: "There is a spectacular relationship. He is an amazing boy. We have to look for a solution to see how he feels comfortable."
Mauro Icardi did earn a start for Argentina, but struggled to have much of an impact as his wait for a first international goal continued.
While the Inter forward is now five games without a goal for his country, Scaloni praised his contribution.
"We tried to integrate him into the team. He did pressure very well and had a couple of interesting moments," he said.
"Mauro made an incredible effort to be here."