How could Enoch have been taken up into heaven before Jesus freed the souls in limbo?

First of all, Jesus didn’t take every soul who ever lived into heaven, only those who had died in God’s friendship, in the state of grace. Secondly, while it’s true that the Old Testament indicates that Enoch as well as Elijah were taken into heaven prior to the atonement and the harrowing of hell, it was still through the merits of Christ’s future passion and death that they were able to go there. Just as the Blessed Virgin was preserved from all stain of sin by the merits of Christ’s future passion applied to her at the time of her conception, in the same way God could bring Enoch and Elijah into heaven by the same future merits of Christ.