So for the Church to pray for unity does not mean that She is denying the unity She already possesses, which is the unity of Faith and obedience to the Chair of St. Peter, but rather She prays that all her members may be united in charity.
There is, however, a heretical denial of the Church's Divinely bestowed unity that must be addressed:
St. Thomas Aquinas, Prima Partis, Q. 76, Art. 2: "...wherefore it is evident that no invincible ignorance is a sin. On the other hand, vincible ignorance is a sin, if it be about matters one is bound to know; but not, if it be about things one is not bound to know."
Antipope Paul VI, Unitatis Redintegratio, #3, cont'd: "For men who believe in Christ and have been truly baptized are in communion with the Catholic Church even though this communion is imperfect. The differences that exist in varying degrees between them and the Catholic Church-whether in doctrine and sometimes in discipline, or concerning the structure of the Church-do indeed create many obstacles, sometimes serious ones, to full ecclesiastical communion. The ecumenical movement is striving to overcome these obstacles. But even in spite of them it remains true that all who have been justified by faith in Baptism are members of Christ's body, and have a right to be called Christian, and so are correctly accepted as brothers by the children of the Catholic Church."
That is a heretical denial of the unity of faith and discipline proper to the Church. It is a denial that only those who profess this faith are able to attain to the fellowship of the children of God, as proven from the following dogmatic definition:
Pope Pius IX, Vatican Council, Session 3, Chapter 3, #8-9, ex cathedra: "Wherefore, by divine and Catholic faith all those things are to be believed which are contained in the word of God as found in Scripture and tradition, and which are proposed by the Church as matters to be believed as divinely revealed, whether by her solemn judgment or in her Ordinary and Universal Magisterium. Since, then, without faith it is impossible to please God and reach the fellowship of his sons and daughters, it follows that no one can ever achieve justification without it, neither can anyone attain eternal life unless he or she perseveres in it to the end."