2007's biopic El Greco claims the painter was put on trial by the Spanish Inquisition, more specifically Grand Inquisitor Fernando Niño de Guevara, for blasphemy. The film is a heavily fictionalized version of the painter's life and doesn't necessarily claim historical accuracy. Nevertheless the tribunal (and acquittal) is the film's major plot element and since it was largely successful (in Greece and Spain), the painter's struggles with the Inquisition are sometimes quoted as fact.
This, however, is quite hard to believe. El Greco would occasionally be invited to tribunals as an interpreter for Greek speaking defendants, and the Grand Inquisitor is most probably the subject of the painter's Portrait of a Cardinal. His relationship with the Inquisition seems to have been generally amicable, and it would have been highly unlikely he could continue producing works with religious themes if he had any kind of troubles with the Catholic Church.
Is there any record of El Greco ever having troubles with the Inquisition during his time in Toledo?