In one case the parents' were fighting so badly that, when they just wouldn't stop, the judge took the child away from both of them and put the child in foster care.
In another case, a SC judge refused to honor a parents' agreement because the GAL claimed that the father was being coerced into agreeing to give up contact against the interests of the child. The alienated father said he desperately wanted to be in his child's life, but he felt he just couldn't force it anymore. He signed an agreement with the mother, but the GAL disagreed and the judge refused to honor the agreement and forced contact with a jail threat to the mother.
There are also many cases where, by law, a judge has to throw out a parental agreement, such as with child support calculation laws. And there are abuse cases, where the judge makes a decision based on the safety of the child, even though the parents have agreed.
Most of the time, a partental agreement is rubber-stamped by the judge, but there are definitely exceptions to that.