How does the Church account for married popes?

Priestly celibacy was made a discipline in the Church by Pope Siricius in the 3rd or 4th Century.

My question is… What of the case of the Borgia Popes; is the Church not aware that Pope Alexander VI(Borgias) was married and had many childrens of which one of them is the then Arch-Bishop of valencia in the 14th century?

Please explain this issue for me… That is one my most contradiction problems I have in my study of ecclesiology. Thanks

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