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When Queen Elizabeth I saw the Tenth Doctor in "The Shakespeare Code" & ordered him killed, it was many years in her timeline after the events shown in "The Day of the Doctor", in which he married her & then (as far as she knew) ran out on her. From her point of view, she was a woman scorned &, as the quotation goes, "Heav'n has no rage like love to hatred turn'd / Nor Hell a fury, like a woman scorn'd," (from the play The Mourning Bride, by William Congreve). Elizabeth I, of course, wasn't merely a woman scorned but was a reigning monarch scorned, making the apparent scorning an act of lèse-majesté (or, perhaps, of high treason).

The Tenth Doctor had no idea why Elizabeth was so furious because, in his timeline, the events of "The Day of the Doctor" hadn't happened yet.