There were several decisions that the Church had to decide upon after the end of the persecutions in the Late Roman Empire, and beginning of the Christian Era. They were handled locally, and where disputes could not be settled, or where there were differences between local churches, General or Ecumenical Councils were (and continue to be) called. The most recent was Vatican II.
Among the decisions regarding the Scriputres was what books should be recognized as Canonical. One of the factors considered was what sources the writers of the Accepted Gospels, and the Epistles who could be attributed to the Apostles used. A main source was the Septuagent, often abbreviated LXX (for the Roman number 70.) As this collection does not contain the books which many Orthodox Bibles include, it was one factor in determining what books to include and exclude from the Canon. There were two Local Councils, (Carthage and Trullo) which did include 3 and 4 Maccabees, and 1 Clement among others. However the Latin Church did not accept them as a pronouncement of the Universal Church, but as part of a Local Council, so not binding. While not formally discussed as part of the third Council of Nicea, many Orthodox Scholars accept that it was discussed by many of the Fathers during the time of that Council and they agreed to accept what those local Councils had accepted, but it was not done formally. Because of this some Orthodox feel the books were accepted by Nicea III, and others don’t. While Roman Catholics accept the books as historical, but not inspired works, suitable for study in order to understand Biblical and Apostolic times, the Catholic Church does not include them in the Canon of the Bible.