With the Oriented Selection set, you can specify the layup direction to add plies on both sides of the surface (shell elements). You can create another Oriented Selection set and flip the direction to apply a ply on the other side of the surface:
Also, the order of plies in the Modeling group matters; the ply at the top will be the first ply applied to the surface, the second ply in the tree, the second building thickness in one direction (depending on the Oriented Selection set), and so on.
ACP’s modeling philosophy is to follow the manufacturing process. How is this part build in real life? How and where are plies applied? If you follow the manufacturing process in ACP, you should be okay.
Note that Ansys employees are not allowed to upload and dowload files on the forum. If you are a commercial customer, you can submit a service request on the Ansys customer portal and we will have a look at your model. Sometimes it is much easier to troubleshoot this way.
Let me know how it goes.