It wasn't only in the garden that Jesus delineated two groups of apostles.
And after six days Jesus taketh Peter, James, and John his brother, and bringeth them up into an high mountain apart, Mt 17:1
And he suffered no man to follow him, save Peter, and James, and John the brother of James. Mk 5:37
And it came to pass about an eight days after these sayings, he took Peter and John and James, and went up into a mountain to pray. Lk 9:28
So, why did this happen? Why was there an apparent inner circle of three among the twelve?
For the Catholic Church, Peter and successors is their visible foundation. This separation is fairly easy to understand.
936 The Lord made St. Peter the visible foundation of his Church. He entrusted the keys of the Church to him. The bishop of the Church of Rome, successor to St. Peter, is "head of the college of bishops, the Vicar of Christ and Pastor of the universal Church on earth" (CIC, can. 331).
But what of James and John?
One reason was the adage that by the mouth of two or three witnesses will something be established (Mt 18:16, Deut 17:6).
Jesus' Transfiguration takes place on a high mountain, before three witnesses chosen by himself: Peter, James and John.
So, this might explain the necessity of an "inner group", but except for Peter's explanation as head, why James and John?
There may be a hint of an explanation here. Jesus foreknew His future and established the care for His mother. James and John sons of Zebedee and Salome who was the sister of Mary were cousins.
If this last supposition is right, Salome was a sister of the Blessed Virgin Mary, and James the Greater and John were first cousins of the Lord; this may explain the discipleship of the two brothers, Salome's request and their own claim to the first position in His kingdom, and His commendation of the Blessed Virgin to her own nephew. But it is doubtful whether the Greek admits of this construction without the addition or the omission of kai (and). Thus the relationship of St. James to Jesus remains doubtful.
James and John were also the first and last apostles to die.
So, from a Catholic point of view, there were three witnesses to prove, one who was the visible foundation of the subsequent Church and two who were most likely cousins to care for Mary.