This could be a problem indeed, particularly when you consider that Christ referred to His 'Church' and not 'Churches'. Christians are those that follow Christ and accept everything He said and did. "Where two or more are gathered in my name, there am I in the midst of them...". True enough. But also, "He who hears you, hears me; he who rejects you rejects me and the One who sent me...", "Thou art Peter and on this rock I will establish my Church...".
In reading Holy Scripture, did you ever consider, for example, how St. Paul in his epistles writes as one who has authority in the name of Christ - and authority given him by Christ Himself? Also, that he writes to whole communities who are united together in Faith under his authority, viz. "Epistle to the Galatians", "1st Epistle to the Corinthians", etc.?
That Christ established a Church and identified Himself so completely with it at a mystical level ("Saul, Saul why do you persecute me..."), and meant for it to be the instrument through which He applies His Grace to fallen humanity, seen in both the individual and collective sense, is undeniable from the testimony of Scripture itself! That this Church is described as His 'body' of which He is the head - and therefore that it must be visible - is also undeniable. That He promised to send, with the Father, the Spirit of Truth to lead Her into all Truth, of which He Himself is, and that He would remain with Her "til the end of the ages" is also attested to in the Holy Scriptures.
The Catholic Church has always throughout history, beginning at the first Pentecost until this very moment, been said Church and only She can, from an historical perspective if nothing else, make this claim. It is in virtue of Christ leading Her through Grace and the Spirit of Truth that She has the authority to canonize, and therefore, recognize the fullness of Holiness among Her members who have "fallen asleep in the Lord" with the public title of Saint.
The Bible records the fact that Jesus founded a Church (not churches) against which the gates of hell would not prevail. His Church has to be unified doctrinally since he tells us to take our disputes to "the Church." Besides, what would be the point of founding many churches with countless, contradictory doctrines?
How can one recognize Christ's Church? It must be One, Holy, Catholic (universal) and Apostolic. We can trace Apostolic succession through the scriptural (Isaiah 22:22, Matthew 16:19, Matthew 23:2-3) and historical fact of the papacy (Chair of Peter).