While Padre Pio was clearly a saint during his life on earth, it doesn't mean he didn't struggle with his own weaknesses.
In particular, it was difficult for Padre Pio to stay calm and collected in the confessional.
In Padre Pio: The True Story, the author explains how the saintly friar would lose his temper and how he regretted it.
One reason Padre Pio would get angry in the confessional was encountering a penitent who was not truly sorry for their sins.
He would also deny absolution to many of these penitents, asking them to come back when they were ready.
A majority of these penitents would return to the confessional, recognizing the weight of their sins and professing true repentance.
Each saint had their own struggles and weaknesses and for Padre Pio, one of those struggles was his "fits of temper" in the confessional.