I don’t know if it was the sealed indictment that was leaked. There were dozens of people who knew he was going to be arrested. It was well planned and exhaustively executed. Someone involved tipped them off.
CNN provided Stone's lawyer with a PDF copy of the sealed indictment hours before the court was notified, even before he had heard from Stone, and hours before it was unsealed by the court. And the copy provided by CNN is identical to the filed version.
It was leaked by somebody with access.
The metadata indicates it was authored by "AAW" which appears to fit Andrew Weissmann of the counsel's office.