Question: "In the Explanation of Matthew by Theophylact, He describes Jesus’ “brothers” as the sons of Cleopas whom Joseph took in after his brother Cleopas died. I never understood that, because I thought Cleopas was still alive after the Resurrection, whereas Joseph died well before Jesus began his ministry. Could you please clarify this apparent contradiction?"
In the Gospels, there are references to a "Cleopas" and a "Clopas":
"Then the one whose name was Cleopas answered and said to Him, “Are You the only stranger in Jerusalem, and have You not known the things which happened there in these days?” (Luke 24:18).
"Now there stood by the cross of Jesus His mother, and His mother’s sister, Mary the wife of Clopas, and Mary Magdalene" (John 19:25),It is usually assumed that Cleopas and Clopas are two forms of the same name. However, while these probably are variant spellings of the same name, whether or not they are the same person is another question. The "Clopas" mention in the Gospel of John is believed to be a brother of St. Joseph, which makes sense, because it is not likely that two sisters from the same parents would both have been named "Mary" and so Mary, the wife of Clopas was the sister-in-law of the Virgin Mary.
There is a tradition that identifies these two men, and so holds that St. Joseph's brother was still living at the time of the crucifixion and resurrection, and was one of the two men who walked with Christ on the road to Emmaus. But a different tradition says that Cleopas, the brother of St. Joseph, had died before St. Joseph, and that his wife and children were taken into the home of St. Joseph. These children are the ones the Gospels speak of as the brothers of the Lord. We find this view laid out by St. Jerome, in his treatise "The Perpetual Virginity of Blessed Mary," which is also supported by the 2nd century Palestinian Christian writer St. Hegesippus. A different tradition, found in the writings of St. Epiphanius of Cyprus, teaches that the brothers of the Lord were the children of St. Joseph from a previous marriage, and so were step-brothers of the Lord. Blessed Theophylact seems to reconcile these two traditions:
"The Lord had brothers and sisters, the children of Joseph which he begat by the wife of his brother Cleopas, for when Cleopas died childless, Joseph took his wife in accordance with the law and had six children by her, four boys and two girls" (The Explanation of the Holy Gospel According to Matthew. Fr. Christopher Stade, Trans. (House Springs, MO: Chrysostom Press, 1992), p. 120).Blessed Theophylact is alluding to the law of Levirate Marriages, found in Deuteronomy 25:5-10. And so he takes a position very similar to that of St. Jerome, but instead of these children being the natural children of Cleopas, he suggests that they were children that St. Joseph fathered on behalf of his dead brother, according to this law. But in any case, what all the traditions of the Church on this matter have in common, in a completely unambiguous way, is that these children were not the children of the Virgin Mary.
For more on this, see: Stump the Priest: The Virgin Mary's "Sister," Mary the Wife of Cleopas