As far as I know, the greater difference is very literalistic and distorted explanation of the foundation of the Church. The Christian Church was founded on the confession of the Lord as the Son of God, that was the confession that Peter was given to express. But the Roman-Catholics at a certain point began to believe that the church was founded on Peter. And moreover that the power was transferred to Peter, and from Him to Popes, ultimating in the idea of the Pope is impeccable when he speaks being on the cathedra. Besides, there are other similarly false ideas about the opening and closing heavens, that the clergy received.
In truth, however, it is the Lord to whom all power was given in heaven and on earth, and not to the Peter (who, according to the letter, was even called Satan in other place of the Gospel). And it is the Lord Alone Jesus Christ who admits into the heavens, and not the clerical order.
From some places in the Gospels it is possible to draw some fallacious conclusions, and thus the understanding of the context is required, and even some knowledge of the spiritual sense of the Word, for apart from only basics can be understood with distortions. There were historically some other deviations, as separation of the bread and the wine during the holy supper.
At the same time, unlike the Protestants, Catholic emphase the role of repentance of life, which is a requirement for salvation, but that can also be distorted by the various doctrines of the meritorious works, the merit belonging to the Lord Alone.
