In the other passages that mention the word Alphaeus (Matthew 10:3, Mark 3:18, Luke 6:16, Acts 1:13) it is in relationship to James, and should be rendered "James of Alphaeus" because the words "son of" is in italics (or in brackets) which means they were added by the translators and are not a part of the original text.
If, on the other hand, these four men were actually offspring of Mary and her husband Joseph as other passages seem to indicate then yes, Jesus had brothers and a sister or two. Matthew 13:55 seems to indicate a need to identify who Jesus is. It would not seem very logical for someone to question the identity of cousins to substantiate someone's identification. When Jesus bestowed upon John the responsibility of caring for his mother, could he have been his cousin too? If so, they were a very closely associated family (see John 19:26).
Matthew 12:46, Mark 3:31 and Luke 8:19 all suggest that Mary and Jesus' other physical family members were all outside waiting to talk to him. If the word for brothers or brethren meant his whole kindred or his fellow citizen, it would have to include the ones who were appealing to him at the door and the ones who were in the crowd. If the word brother meant just the sons of his aunt Mary the wife of Cleophas / Clopas / Alphaeus then why not his mother at the door and why would the door man think that he should want to stop what he was doing to speak to them. The person at the door was indeed his own mother because that would be the only person who would be important enough for any man to stop an important lecture to speak with her. Aunts and cousins could wait until he was finished with whatever he was doing, but only a mother would be bringing some kind of news he needed to know urgently. Once James the Less is identified and who his parents were, we will find that the Bible aligns him with Simon, Joses, Jude (Judas) and at least a sister named Salome. Sister Salome is identified in Mark 15:40 and 16:1 as the child of one of the Mary's who came to see Jesus crucified as well as visit his tomb. She and brother Joses were together with one of the Mary's observing Jesus on the cross.
If Salome and James were with their mother, and their mother Mary was in fact Mary the aunt of Jesus, they could technically be his brothers and sisters.
"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, see also Matthew 27:55 - 56)
The only scripture verse which includes all three people named Mary into one is John 19:25, which indicates that Jesus' mother had a sister-in-law or sisters, one of whom is named Mary whose husband was Cleophas (Clopas). The Bible does not state, however, that she was James the Less' mother.
So then we come to a passage in Acts 1:14 which says the following.
"These all continued with one accord in prayer and supplication, with the women and Mary the mother of Jesus, and with His brothers." (Acts 1:14, NKJV)
Why would the mother of Jesus be here with the rest of the church if she had not been the same one who cared for the body and watched from afar? Her other two sons Jude and James were also disciples of the first apostolic church and wrote epistles to the brethren that are in the canonized Scripture. In Matthew 12:46-50 Jesus is contrasting his physical family who people knew versus those he considered to be his SPIRITUAL family members - those who had been called out of this world by his heavenly Father.
Nowhere does it say that Mary and the men called Simon, James, Judas, and Joses cannot be the mother and brothers of Jesus. In fact, one other scripture lists ALL the physical family members of Jesus by name and lets us know that He had a sister or two. During his ministry, Christ and the disciples traveled from Capernaum to Nazareth (where he grew up and lived until the age of thirty). When the Sabbath day came, he taught in the local synagogue. Those who heard his preaching KNEW his earthly family and some no doubt actually saw him grow up from a boy to a man! Their responses to his words are both revealing and a bit sad (Mark 6:1 - 3, see also Matthew 13:54 - 57).Those in Nazareth did not accept Jesus' words strictly in the light of scripture. Instead, they reasoned that somebody they lived near and whose family they knew quite well COULD NOT possibly be special or closer to God than they were! They rejected his message because they FIRST found reasons to reject HIM! Though a sad testament to human nature, these verses do show that the MANY locals who heard our Savior teach in Nazareth were quite knowledgeable about the composition of his earthly family.
In conclusion, Jesus DID have brothers and sisters --- in fact, several of them! Including him, Mary gave birth to FIVE boys and at least TWO girls, for a family of SEVEN children!