And the explanation of the evidence that the Prophet Muhammad (peace be upon him) ordered the killing of certain crows. He did not order the killing of all crows.
Lady Aisha (may Allah be pleased with her) narrates from the Prophet (peace and blessings be upon him) that he said: "There are five harmful animals that may be killed both inside and outside the Haram: the snake, the speckled crow, the mouse, the biting dog, and the kite (a type of bird of prey)."
Hadith Referenceصحيح ابن خزيمه / جماع أبواب ذكر أفعال اختلف الناس فى إباحته للمحرم، نصت سنة النبى صلى الله عليه وسلم أو دلت على إباحتها / 2669