If John XXIII misunderstood Padre Pio because of misinformation, that still has nothing to do with John’s performance of heroic virtue, his sanctity.
Aldo Cazzullo, a writer on religious affairs, noted that John XXIII - the former Angelo Roncalli - had “disliked and mistrusted” Padre Pio since he travelled in Apulia in the 1920s, regarding the friar’s “almost medieval mystical faith” as at odds with his own modernist outlook. In the 1960 memorandum the Pope says he feels “privileged to be free of the contamination which for forty years has clung to hundreds of thousands of souls who have been stupefied and disturbed to an unbelievable degree.”
http://www.beliefnet.com/columnists/deaconsbench/2007/10/was-padre-pio-a-fraud.html