One of the main contentions about the confession is in Chapter 26.4. I know many people have a problem with chapter 26 and the Roman Pope being called anti-Christ.
4. The Lord Jesus Christ is the Head of the church, in whom, by the appointment of the Father, all power for the calling, institution, order or government of the church, is invested in a supreme and sovereign manner; neither can the Pope of Rome in any sense be head thereof, but is that antichrist, that man of sin, and son of perdition, that exalteth himself in the church against Christ, and all that is called God; whom the Lord shall destroy with the brightness of his coming.
( Colossians 1:18; Matthew 28:18-20; Ephesians 4:11, 12; 2 Thessalonians 2:2-9 )
Concerning the Anti-Christ I find Matthew Winzer's explanation on the WCF on this topic to be very beneficial and I can put my fingers around it.
Reverend Matthew Winzer stated to me and I agree with him concerning Chapter 26.4.
This is a little off topic, but the Holy Spirit speaks of many antichrists as well as the antichrist. I think the Confession is quite right to do so. But as I've had cause to say before, chapter 25 of the Confession is dealing with ecclesiology not eschatology. Propositionally therefore the statement about the antichrist only requires us to affirm (1.) that Christ alone is the head of the church, (2.) that the antichrist falsely assumes that headship, and (3.) the Pope, in falsely assuming that headship, acts as the antichrist. It's worth pointing out that because the confessional statement interprets the apostle's language as referring to a system rather than an individual man, it leaves open the possibility of a future development of the antichristian system of Papal Rome.