Why is the Church not perfect?

Christianity is not perfect. The Church is not perfect.

It is the Christians that cause the imperfections of Christianity.  It is the church members, including the leaders, who are the reason that the church often disappoint people.

Jesus said the Kingdom of God may be compared to someone who sowed good seed in his field, but while everyone was asleep, someone else sowed weeds among the wheat. When both began to grow, the workers asked the farmer where the weeds came from. He answered, "An enemy did this" (Mt 13:28). And when they asked him if they should destroy the weeds, he said, (Mt 13:29-30) "No ... because while you are pulling the weeds, you may root up the wheat with them. (30) Let both grow together until the harvest. At that time I will tell the harvesters: First collect the weeds and tie them in bundles to be burned; then gather the wheat and bring it into my barn."

Wheat and weed grow together in the Church. Jesus told the parable to warn his people that they have evil living amongst them.  He offered a promise that God will decisively deal with wickedness and sin in the church.

This parable warns against accepting Jesus as Saviour without accepting him as Lord. Some believe that Jesus died on the cross to save them from judgement. Yet they would not accept him as their Master, Lord and King. They are the weeds in God’s Kingdom fields. At the end of the age they will be pulled out. They will not be part of the harvest. Because we cannot claim that Jesus saved us, yet act as if he doesn't own us.

The parable ends with the righteous that rejoice in Christ as their King and Head and in obedience to him bear much fruit for his Kingdom.   We are told that they eternally "will shine like the sun in the kingdom of their Father." (Matt 13:43).