Guardiola, 54, was clearly unhappy with the Crystal Palace shot stopper, confronting him after the final whistle.
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Henderson should arguably have been sent off in the first half after he appeared the handle the ball outside of the box and deny Erling Haaland a goalscoring opportunity.
The England international went on to save Omar Marmoush’s 33rd minute penalty and Palace clung on to secure their first ever piece of major silverware.
As a result of their FA Cup win, Oliver Glasner’s side will also play in next season’s Europa League, the first time Palace have ever comepeted in Europe.